JP2013523650A - RNA interference in ocular applications - Google Patents

Abstract

The present invention relates to the administration of sd-rxRNA and rxRNAori molecules to the eye.

Description

Related Applications This application is filed in US Provisional Application No. US 61 / 317,254, filed Mar. 24, 2010, entitled “RNA Interference in Eye Applications”, and US Provisional Application No. US 61 / 317,621, claiming the benefit according to 35 USC § 119 (e) of the title “RNA interference in ocular applications”, the entire disclosures of which applications are incorporated herein by reference in their entirety.

The present invention relates to the field of RNA interference (RNAi). The present invention more particularly relates to the administration of nucleic acid molecules having improved in vivo delivery properties to the eye and their use in efficient gene silencing.

Background of the Invention Complementary oligonucleotide sequences are promising therapeutic agents and useful research tools in elucidating gene function. However, prior art oligonucleotide molecules suffer from a number of problems that may hinder their clinical development, which in vivo gene expression (protein synthesis) using such compositions. It is often difficult to achieve the intended efficient inhibition of

  A major problem has been the delivery of these compounds to cells and tissues. Conventional double-stranded RNAi compounds are 19-29 bases long and form a highly negatively charged strong helix with a size of approximately 1.5 × 10-15 nm. This rod-shaped molecule cannot penetrate the cell membrane and as a result has very limited potency both in vitro and in vivo. Consequently, all conventional RNAi compounds require some kind of delivery vehicle to promote their tissue distribution and cellular uptake. This is believed to be a major limiting factor for RNAi technology.

  Previously, there have been attempts to apply chemical modifications to oligonucleotides to improve their cellular uptake properties. One such modification was the attachment of cholesterol molecules to oligonucleotides. The first report on this approach was by Letsinger et al. In 1989. Later, ISIS Pharmaceuticals, Inc. (Carlsbad, CA) reported a more advanced technique for attaching cholesterol molecules to oligonucleotides (Manoharan, 1992).

  With respect to the discovery of siRNA in the late 90s, similar types of modifications were attempted on these molecules to enhance their delivery profile. Cholesterol molecules bound to slightly modified (Soutschek, 2004) and heavily modified (Wolfrum, 2007) siRNAs have appeared in the literature. Yamada et al. (2008) also reported the use of advanced linker compounds that improved cholesterol-mediated siRNA uptake. Despite this effort, the uptake of these types of compounds is inhibited in the presence of biological fluids, which greatly limits their efficacy in gene silencing in vivo, and the applicability of these compounds in clinical settings Is considered to be limited.

  Described herein are methods and compositions for efficient in vivo administration of sd-rxRNA molecules to the eye. Surprisingly, intraocular (eg, intravitreal and subretinal) administration of sd-rxRNA molecules resulted in distribution and uptake of sd-rxRNA by all cell layers in the retina. These molecules have a wide range of applications for the treatment of diseases or disorders associated with the eye.

  Aspects of the invention relate to a method for delivering a nucleic acid to an eye of a subject in need thereof, wherein the method targets sd-rxRNA in an effective amount to promote RNA interference by the sd-rxRNA in the eye Administration to the eyes. In some embodiments, administration of sd-rxRNA is intravitreal.

  In some embodiments, the method is for treating an eye disorder. In certain embodiments, the ocular disorder is vascular leakage, angiogenesis, age-related macular degeneration (AMD), choroidal neovascularization (wet AMD), geographic atrophy (advanced dry) AMD), Early-to-intermediate dry AMD, postoperative cystoid macular edema (CME), nonproliferative diabetic retinopathy (NPDR), diabetic macular edema (DME), retinal vein occlusion (RVO) ) Secondary macular edema, proliferative diabetic retinopathy (PDR), glaucoma, neovascular glaucoma (NVG), retinopathy of prematurity (ROP), fibroproliferative retinal disease, proliferative vitreoretinopathy (PVR), Epiretinal / vitreous macular adhesion, retinal degenerative disease, retinitis pigmentosa, retinal vascular occlusion, retinal vein occlusion, retinal artery occlusion, retinoblastoma, trabeculectomy due to scar formation Failure or uveitis. In one embodiment, the ocular disorder is AMD. In another embodiment, the ocular disorder is DME. In yet another embodiment, the eye disorder is PVR. In yet another aspect, the ocular disorder is trabeculectomy failure due to scar formation.

  In certain embodiments, sd-rxRNA is VEGF, MAP4K4, PDGF-B, SDF-1, IGTA5, ANG2, CTGF, HIF-1α, mTOR, SDF-1, PDGF-B, SPP1, PTGS2 (COX-2), Directed to genes encoding TGFβ1, TGFβ2, complement factor 3 or 5, PDGFRa, PPIB or myc or combinations thereof.

  In some embodiments, the sd-rxRNA is directed against a gene encoding VEGF. In certain embodiments, the sd-rxRNA is directed against a sequence selected from the sequences in Table 2. In one embodiment, the sd-rxRNA is directed against at least 12 consecutive nucleotides of a sequence selected from the sequences in Table 2. In another embodiment, the sd-rxRNA comprises at least 12 contiguous nucleotides of a sequence selected from the sequences in Tables 3-8 or 10. In yet another embodiment, the sense strand of sd-rxRNA comprises at least 12 contiguous nucleotides of the sequence of SEQ ID NO: 1317 or SEQ ID NO: 1357. In yet another embodiment, the antisense strand of sd-rxRNA comprises at least 12 contiguous nucleotides of the sequence of SEQ ID NO: 1318 or SEQ ID NO: 1358. In a further embodiment, the sense strand of sd-rxRNA comprises SEQ ID NO: 1317 and the antisense strand of sd-rxRNA comprises SEQ ID NO: 1318. In one embodiment, the sense strand of sd-rxRNA comprises SEQ ID NO: 1357 and the antisense strand of sd-rxRNA comprises SEQ ID NO: 1358. In another embodiment, the sense strand of sd-rxRNA comprises SEQ ID NO: 1379 and the antisense strand of sd-rxRNA comprises SEQ ID NO: 1380. In yet another embodiment, the sense strand of sd-rxRNA comprises SEQ ID NO: 1397 and the antisense strand of sd-rxRNA comprises SEQ ID NO: 1398.

  In certain embodiments, the sd-rxRNA is directed against a gene encoding CTGF. In one embodiment, the antisense strand of sd-rxRNA comprises at least 12 contiguous nucleotides of the sequence of SEQ ID NO: 948 or SEQ ID NO: 964. In another embodiment, the sense strand of sd-rxRNA comprises at least 12 contiguous nucleotides of the sequence of SEQ ID NO: 947 or SEQ ID NO: 963.

  In some embodiments, two or more different sd-rxRNAs directed against genes encoding two or more different proteins are administered together to the eye of the subject. In one embodiment, sd-rxRNA is directed against VEGF and CTGF. In another embodiment, the sd-rxRNA is directed against VEGF and PTGS2 (COX-2).

In certain aspects, the sd-rxRNA of any of the above embodiments is hydrophobically modified. In some embodiments, the sd-rxRNA is bound to one or more hydrophobic conjugates.
In certain aspects, the sd-rxRNA of any of the above embodiments comprises at least one 5-methyl C or U modification.

  Another aspect of the invention relates to a method for delivering a nucleic acid to the eye of a subject in need thereof, wherein the method comprises rxRNAori in the eye in an effective amount to promote RNA interference by rxRNAori in the eye. Administration. In one embodiment, rxRNAori is directed against VEGF. In another embodiment, rxRNAori is directed against a sequence comprising at least 12 consecutive nucleotides of a sequence selected from the sequences in Table 2. In yet another embodiment, the sense strand of rxRNAori comprises at least 12 contiguous nucleotides of the sequence of SEQ ID NO: 13 or SEQ ID NO: 28. In yet another embodiment, the antisense strand of rxRNAori comprises at least 12 contiguous nucleotides of the sequence of SEQ ID NO: 1377 or SEQ ID NO: 1378.

  Some aspects of the invention relate to sd-rxRNAs directed to sequences selected from the sequences in Table 2. Another aspect relates to sd-rxRNA directed to a sequence comprising at least 12 contiguous nucleotides of a sequence selected from the sequences in Table 2. Yet another aspect relates to sd-rxRNA comprising at least 12 consecutive nucleotides of a sequence selected from the sequences in Tables 3-8 or 10. In some embodiments, the sense strand of sd-rxRNA comprises at least 12 contiguous nucleotides of the sequence of SEQ ID NOs: 1317, 1357, 1379, or 1397. In other embodiments, the antisense strand of sd-rxRNA comprises at least 12 contiguous nucleotides of the sequence of SEQ ID NOs: 1318, 1358, 1380, or 1398. In yet other embodiments, the antisense strand of sd-rxRNA comprises SEQ ID NO: 1318. In yet other embodiments, the sense strand of sd-rxRNA comprises SEQ ID NO: 1357 and the antisense strand of sd-rxRNA comprises SEQ ID NO: 1358. In a further embodiment, the sense strand of sd-rxRNA comprises SEQ ID NO: 1379 and the antisense strand of sd-rxRNA comprises SEQ ID NO: 1380. In yet a further embodiment, the sense strand of sd-rxRNA comprises SEQ ID NO: 1397 and the antisense strand of sd-rxRNA comprises SEQ ID NO: 1398. In certain embodiments, the sd-rxRNA is hydrophobically modified. In other embodiments, the sd-rxRNA is bound to one or more hydrophobic conjugates. In certain other embodiments, the sd-rxRNA comprises at least one 5-methyl C or U modification.

  Another aspect of the present invention relates to a composition comprising sd-rxRNA of any one of the above aspects or embodiments. In one embodiment, the composition further comprises sd-rxRNA directed against a gene encoding a protein other than VEGF. In another embodiment, the composition comprises sd-rxRNA directed against a gene encoding CTGF and / or PTGS2 (COX-2).

  Aspects of the invention also relate to rxRNAori directed against a sequence selected from the sequences in Table 2. Another aspect relates to rxRNAori directed against a sequence comprising at least 12 consecutive nucleotides of a sequence selected from the sequences in Table 2. In one embodiment, the sense strand of rxRNAori comprises at least 12 contiguous nucleotides of the sequence of SEQ ID NO: 13 or SEQ ID NO: 28. In another embodiment, the antisense strand of rxRNAori comprises at least 12 contiguous nucleotides of the sequence of SEQ ID NO: 1377 or SEQ ID NO: 1378.

  Another aspect of the invention relates to a composition comprising rxRNAori of any one of the above aspects or embodiments. In one embodiment, the composition comprises rxRNAori directed against a gene encoding a protein other than VEGF. In another embodiment, the composition comprises rxRNAori directed against a gene encoding CTGF and / or PTGS2 (COX-2).

  In some embodiments, the sd-rxRNA in the composition is hydrophobically modified. In certain embodiments, the sd-rxRNA is bound to one or more hydrophobic conjugates. In some embodiments, the sd-rxRNA is bound to a lipophilic group. In certain embodiments, the lipophilic group is attached to the passenger strand of the sd-rxRNA. In some embodiments, the sd-rxRNA is bound to cholesterol, a long chain alkyl cholesterol analog, vitamin A or vitamin E. In some embodiments, the sd-rxRNA is conjugated to a chloroformate.

  The sd-rxRNA may comprise at least one 2'O methyl or 2 'fluoro modification and / or at least one 5-methyl C or U modification. In some embodiments, the sd-rxRNA has a guide strand that is 16-28 nucleotides in length. In certain embodiments, at least 40% of the nucleotides of the sd-rxRNA are modified. The sd-rxRNA may be attached to a linker, which in some embodiments is protonatable.

  In some embodiments, the sd-rxRNA comprises at least two single stranded regions, which may comprise phosphorothioate modifications. In certain embodiments, the single stranded region is located at the 3 'end of the guide strand and the 5' end of the passenger strand.

  Each of the limitations of the invention can encompass various aspects of the invention. Thus, it is understood that each of the limitations of the invention including any one element or combination of elements can be included in each aspect of the invention. The present invention is not limited in its application to the details of construction and the arrangement of components set forth in the following description or illustrated in the drawings. The invention may be practiced or carried out in other ways and in a variety of ways.

BRIEF DESCRIPTION OF THE DRAWINGS The accompanying drawings are not intended to be drawn to scale . In the drawings, each identical or nearly identical component that is illustrated in various figures is represented by a like numeral. Not all components are labeled in all drawings for purposes of clarity. In the drawing, it is as follows.

FIG. 1 represents DIC, DY547 and Hoechst confocal triple images showing that sd-rxRNA penetrated the entire retina by 24 hours after intravitreal or subretinal administration. FIG. 2 shows that sd-rxRNA improved retinal delivery over rxRNAori. The upper panel represents an image obtained immediately after administration, showing intravitreal delivery of sd-rxRNA and rxRNAori. The middle and lower panels represent fluorescent images obtained 24 and 48 hours after administration, respectively, indicating retinal delivery of sd-rxRNA only.

FIG. 3 shows that after intravitreal administration of sd-rxRNA, a fluorescent signal is detected throughout the retina, but not after administration of PBS or rxRNAori. FIG. 4 shows that sd-rxRNA penetrates the retina into the outer segment of the photoreceptor. FIG. 5 shows the strong uptake and thereby silencing of sd-rxRNA in ARPE-19 cells compared to the uptake and thereby silencing of rxRNAori in ARPE-19 cells.

FIG. 6 shows a non-limiting example of sd-rxRNA with potential in the eye. The optimized lead molecules in FIG. 6 correspond to the following SEQ ID NOs representing the sense and antisense strands, respectively: lead 21212: SEQ ID NO: 963 and 964; lead 21214: SEQ ID NO: 967 and 968; lead 21215: SEQ ID NO: Lead 21204: SEQ ID NO: 947 and 948; lead 21205: SEQ ID NO: 949 and 950; lead 21227: SEQ ID NO: 993 and 994; lead 21381: SEQ ID NO: 1011 and 1012; lead 21382: SEQ ID NO: 1013 and 1014; lead 21429: SEQ ID NO: 1303 and 1024; lead 21430: SEQ ID NO: 1025 and 1026; lead 21383: SEQ ID NO: 1015 and 1016; lead 21224: SEQ ID NO: 987 and 988; lead 21228: SEQ ID NO: 1399 and 1400; lead 21229: SEQ ID NO: 1401 Lead 21230: SEQ ID NO: 1403 and 1404; lead 21393: SEQ ID NO: 1405 and 1406; lead 21394: SEQ ID NO: 1407 and 1408; lead 21233: SEQ ID NO: 1409 and 1410; lead 21234: SEQ ID NO: 1411 and 1412; lead 21360: SEQ ID NO: 1413 and 1414; lead 21374: SEQ ID NO: 1304 and 1314; lead 21366: SEQ ID NO: 1415 and 1416; lead 21368: SEQ ID NO: 1417 and 1418; lead 21379: SEQ ID NO: 1155 and 1156; lead 21380: SEQ ID NO: 1157 and 1158; lead 21352: SEQ ID NO: 1419 and 1420; and lead 21777: SEQ ID NO: 1421.

FIG. 7 shows the identification of VEGF sd-rxRNA. FIG. 8 shows the progression of sd-rxRNA penetration into the ocular cell layer after intravitreal administration. The sd-rxRNA penetrates into the ganglion cell layer by 2 to 3 hours after administration. The sd-rxRNA penetrates into the retinal pigment epithelium (RPE) and photoreceptor outer segments by 24 hours after administration. FIG. 9 shows by confocal microscopy that sd-rxRNA penetrates the outer segments of RPE and photoreceptors while there is no visible penetration of conventional RNAi compounds.

FIG. 10 shows that fluorescent sd-rxRNA can be detected in all rabbit retinal cell layers 24 hours after administration, but rxRNAori cannot be detected. FIG. 11 presents a confocal image at high magnification showing that sd-rxRNA penetrates all rabbit retinal cell layers 24 hours after administration. FIG. 12 shows in vivo dose-dependent silencing after intravitreal administration with sd-rxRNA.

FIG. 13 shows the period of silencing of PPIB by sd-rxRNA in mouse eyes. FIG. 14 shows the duration of MAP4K4 silencing by sd-rxRNA in mouse eyes. FIG. 15 shows that sd-rxRNA does not cause vascular leakage 3 weeks after administration. FIG. 16 shows that sd-rxRNA does not cause structural damage after 3 weeks of administration. FIG. 17 demonstrates that sd-rxRNA does not impair retinal function 3 weeks after administration. FIG. 18 shows that multiple sd-rxRNA constructs can be used to target multiple genes simultaneously.

FIG. 19 shows that linker chemistry variations do not affect sd-rxRNA silencing activity in vitro. To determine the chemistry of two different linkers, hydroxyproline linker and ribolinker, for self-delivery in passive uptake assays for multiple sd-rxRNAs (targeting Map4k4 or PPIB) It was evaluated. HeLa cells were transfected with sd-rxRNA at 1 uM, 0.1 uM or 0.01 uM for 48 hours in the absence of delivery vehicle (passive transfection). Use of either linker results in effective delivery of sd-rxRNA.

DETAILED DESCRIPTION aspect of the present invention relates to methods and compositions involved in gene silencing. The present invention states that, at least in part, delivery of sd-rxRNA to the eye, including subretinal and intravitreal injection, results in efficient distribution and uptake by all cell layers in the retina, including the retinal pigment epithelial layer. Based on amazing discoveries. For sd-rxRNA, dramatically better retina uptake and distribution is observed than for conventional RNAi compounds. Thus, sd-rxRNA represents a new class of therapeutic RNAi molecules with great potential in the treatment of ocular conditions or disorders.

Sd-rxRNA molecules Aspects of the invention relate to sd-rxRNA molecules. As used herein, “sd-rxRNA” or “sd-rxRNA molecule” refers to PCT Publication No. WO2010 / 033247 (Application No. PCT / US2009 / 005247), filed on Sep. 22, 2009, title It relates to self-delivering RNA molecules, such as those described in “REDUCED SIZE SELF-DELIVERING RNAI COMPOUNDS”, which are hereby incorporated by reference. Briefly, sd-rxRNA (also referred to as sd-rxRNA ^nano ) is an isolated asymmetric double-stranded nucleic acid molecule having a guide strand with a length of at least 16 nucleotides, and 8 Comprising a passenger strand of ˜18 nucleotides in length, wherein said double stranded nucleic acid molecule has a double stranded region and a single stranded region, wherein the single stranded region is 4-12 nucleotides long. And has a backbone modification of at least 3 nucleotides. In a preferred embodiment, the double stranded nucleic acid molecule has one end that is either blunt or contains one or two nucleotide overhangs. The sd-rxRNA molecule may be optimized through chemical modification and in some instances through the attachment of hydrophobic conjugates.

  In some embodiments, the sd-rxRNA comprises an isolated double stranded nucleic acid molecule comprising a guide strand and a passenger strand, wherein the region of the molecule that is double stranded is 8-15 nucleotides in length. Wherein the guide strand comprises a single stranded region that is 4-12 nucleotides in length, wherein the single stranded region of the guide strand is 3, 4, 5, 6, 7, 8, 9, 9, 11 or 12 phosphorothioate modifications, and wherein at least 40% of the nucleotides of the double stranded nucleic acid are modified.

The polynucleotides of the present invention are herein referred to as isolated double stranded or duplex nucleic acids, oligonucleotides or polynucleotides, nanomolecules, nanoRNAs, sd-rxRNA ^nano , sd- referred to as rxRNA or RNA molecule.

  sd-rxRNA is taken up by cells much more efficiently compared to conventional siRNA. These molecules are highly efficient in silencing target gene expression and have higher activity in the presence of serum, efficient self-delivery, diverse linkers and RNAi molecules compared to the previously described RNAi molecules. Provides significant advantages, including the compatibility of and the reduced or complete absence of chemical modifications associated with toxicity.

  In contrast to single-stranded polynucleotides, duplex polynucleotides have traditionally been difficult to deliver to cells due to their robust structure and multiple negative charges that make membrane transport difficult. However, despite being partially double-stranded, sd-rxRNA is recognized as a single strand in vivo and can be efficiently delivered across the cell membrane. As a result, the polynucleotides of the present invention are capable of self-delivery in many instances. Thus, the polynucleotides of the invention may be formulated in a manner similar to conventional RNAi agents, or they may be delivered to cells or subjects alone (or with a non-deliverable carrier) for self-delivery. . In one embodiment of the invention, a self-delivering asymmetric double-stranded RNA molecule is provided, wherein a portion of the molecule is similar to a conventional RNA duplex and the second portion of the molecule is single stranded. .

  The oligonucleotides of the invention, in some aspects, have a combination of an asymmetric structure comprising a double stranded region and a single stranded region of 5 nucleotides or longer and a specific chemical modification pattern, and are lipophilic or Conjugated to a hydrophobic molecule. This class of RNAi-like compounds has excellent potency in vitro and in vivo. The combination of a reduced size of the robust duplex region and the phosphorothioate modification applied to the single stranded region is believed to contribute to the superior efficacy observed.

  The present invention is based, at least in part, on the surprising discovery that sd-rxRNA can be efficiently delivered to the eye through either subretinal or intravitreal injection. Based on results generated in several different mammalian systems, including mice, rats and rabbits, as presented in the examples section, more dramatic after administration of sd-rxRNA than after administration of conventional RNAi compounds. Thus, better (up to several times) better ocular uptake and distribution is observed.

  Another surprising aspect of the present invention is that sd-rxRNA molecules are taken up by all cell layers in the retina, including the retinal pigment epithelial cell layer. Through both subretinal and intravitreal injection, an efficient sd-rxRNA distribution is achieved, and both methods of administration are compatible with aspects of the invention. In some embodiments, intravitreal administration is preferred due to technical ease and widespread use in intraocular drug delivery.

  As used herein, “ocular” refers to the eye and any and all of its cells, including muscles, nerves, blood vessels, lacrimal ducts, membranes, etc., and the eye and its physiology. Includes structures associated with functional functions. The terms ocular and eye are used interchangeably throughout this disclosure. Non-limiting examples of intraocular cell types include: cells located in the ganglion cell layer (GCL), inner plexiform layer (IPL), inner granular layer (INL), outer reticular layer (OPL) ), Outer granule layer (ONL), rod and cone outer segment (OS), retinal pigment epithelium (RPE), rod and cone inner segment (IS), conjunctival epithelium, iris, Ciliary body, keratin, and epithelium of the sebaceous glands of the eye.

  In a preferred embodiment, the RNAi compound of the present invention comprises an asymmetric compound comprising a duplex region (required for efficient RISC entry and 8-15 bases long) and a single stranded region 4-12 nucleotides long. Including. In some embodiments, the duplex region is 13 or 14 nucleotides in length. A single-stranded region of 6 or 7 nucleotides is preferred in some embodiments. The single stranded region of the novel RNAi compound also contains 2-12 phosphorothioate internucleotide linkages (referred to as phosphorothioate modifications). 6-8 phosphorothioate internucleotide linkages are preferred in some embodiments. Furthermore, the RNAi compounds of the present invention also contain a unique chemical modification pattern, which provides stability and is compatible with RISC invasion. The combination of these factors resulted in unexpected properties that are highly useful for the delivery of RNAi agents in vitro and in vivo.

  Chemical modification patterns that provide stability and are compatible with RISC entry include modifications to the sense or passenger strand, as well as to the antisense or guide strand. For example, the passenger strand may be modified with any chemical entity that ensures stability and does not interfere with activity. Such modifications include 2 'ribo modifications (O-methyl, 2'F, 2 deoxy and others), and backbone modifications such as phosphorothioate modifications. A preferred chemical modification pattern in the passenger strand includes O-methyl modification of C and U nucleotides in the passenger strand. Alternatively, the passenger strand may be completely O-methyl modified.

  The guide strand may be modified, for example, by any chemical modification that ensures stability without interfering with RISC entry. Preferred chemical modification patterns in the guide strand include those in which the majority of C and U nucleotides are 2'F modified and the 5 'end is phosphorylated. Another preferred chemical modification pattern in the guide strand includes 2'O methyl modification at position 1, and C / U at positions 11-18, and chemical phosphorylation at the 5 'end. Yet another preferred chemical modification pattern in the guide strand is 2′O methyl modification at position 1, and C / U at positions 11-18, and chemical phosphorylation at the 5 ′ end, and C / U at positions 2-10. The 2'F modification is mentioned. In some embodiments, the passenger strand and / or guide strand comprises at least one 5-methyl C or U modification.

  In some embodiments, at least 30% of the nucleotides in the sd-rxRNA are modified. For example, at least 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43 of nucleotides in sd-rxRNA %, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76% 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93 %, 94%, 95%, 96%, 97%, 98% or 99% are modified. In some embodiments, 100% of the nucleotides in the sd-rxRNA are modified.

  The above chemical modification pattern of the oligonucleotides of the present invention was well tolerated and actually improved the potency of asymmetric RNAi compounds. It has also been shown experimentally herein that the combination of modifications to RNAi results in achieving optimal efficacy in passive uptake of RNAi when used with polynucleotides. Removal or size reduction of any of the components described (guide strand stabilization, phosphorothioate extension, sense strand stabilization and hydrophobic conjugates), in some cases, results in sub-optimal efficacy In some cases, this results in a complete loss of efficacy. The combination of elements leads to the development of compounds that are fully active after delivery to cells such as HeLa cells. The data in the examples presented below demonstrate high efficacy upon ocular administration of the oligonucleotides of the invention.

  sd-rxRNA can be further improved in some instances by improving the hydrophobicity of the compound using a novel type of compound. For example, one compound relates to the use of hydrophobic base modification. Any base at any position can be modified as long as the modification results in an increase in the base partition coefficient. Preferred positions for the modifying compound are the 4th and 5th positions of the pyrimidine. The main advantages of these positions are (a) ease of synthesis, and (b) interference with base pairing and A form helix formation, which is essential for RISC complex loading and target recognition. There is no. A version of the sd-rxRNA compound was used in which multiple deoxyuridines were present without interfering with the overall compound efficacy. Furthermore, major improvements in tissue distribution and cellular uptake can be obtained by optimizing the structure of the hydrophobic conjugate. In some preferred embodiments, the structure of the sterol is modified to change (increase / decrease) the C17 attached chain. This type of modification results in a significant increase in cellular uptake and improved tissue uptake properties in vivo.

  The dsRNA formulated according to the present invention also includes rxRNAori. rxRNAori is RNA described in PCT Publication No. WO2009 / 102427 (Application No. PCT / US2009 / 000852) and title “MODIFIED RNAI POLYNUCLEOTIDES AND USES THEREOF” filed on February 11, 2009, and incorporated as a reference from now on Refers to the class of molecules.

  In some embodiments, the rxRNAori molecule comprises a 12-35 nucleotide long double stranded RNA (dsRNA) construct for inhibiting target gene expression, the construct having a 5 ′ end and a 3 ′ end. Sense strand, where the sense strand is highly modified with a 2′-modified ribose sugar, and 3-6 nucleotides in the middle of the sense strand are now with a 2′-modified ribose sugar Unmodified) and an antisense strand having a 5 ′ end and a 3 ′ end that hybridizes to the sense strand and mRNA of the target gene, wherein the dsRNA is in a sequence-dependent manner. Inhibits expression of the target gene.

  rxRNAori may include any of the modifications described herein. In some embodiments, at least 30% of the nucleotides in rxRNAori are modified. For example, at least 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43% of the nucleotides in rxRNAori, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60% 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77 %, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% are modified. In some embodiments, 100% of the nucleotides in the sd-rxRNA are modified. In some embodiments, only the passenger strand of rxRNAori contains the modification.

  The present invention is not limited in its application to the details of construction and the arrangement of components set forth in the following description or illustrated in the drawings. The invention may be practiced or carried out in other ways and in a variety of ways. Also, the terms and terminology used herein are for the purpose of explanation and should not be considered limiting. The use of “including”, “comprising”, or “having”, “containing”, “involving”, and variations thereof herein is And the equivalents thereof, as well as additional items.

  Accordingly, aspects of the invention relate to an isolated double stranded nucleic acid molecule comprising a guide (antisense) strand and a passenger (sense) strand. As used herein, the term “duplex” refers to 1 or 2 in which at least a portion of the nucleomonomers (nucleomonomers) are complementary and hydrogen bonded to form a double stranded region. It refers to the above nucleic acid molecule. In some embodiments, the length of the guide strand ranges from 16 to 29 nucleotides in length. In certain embodiments, the guide strand is 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, or 29 nucleotides in length. The guide strand is complementary to the target gene. Complementarity between the guide strand and the target gene can exist over any part of the guide strand. As used herein, complementarity is more incomplete complementarity, even complete complementarity, so long as the guide strand is sufficiently complementary to mediate RNAi to the target. It may be. In some embodiments, complementarity is a mismatch of less than 25%, 20%, 15%, 10%, 5%, 4%, 3%, 2%, or 1% between the guide strand and the target Point to. Perfect complementarity refers to 100% complementarity. Thus, the present invention has the advantage of being able to tolerate sequence changes that can be predicted due to genetic mutation, strain polymorphism, or evolutionary branching. For example, siRNAs with insertions, deletions, and single point mutations compared to the target sequence have also been found to be effective for inhibition. Furthermore, not all sites of siRNA contribute equally to target recognition. The mismatch at the center of the siRNA is most important and essentially abolishes cleavage of the target RNA. With respect to the antisense strand, mismatches upstream of the center or upstream of the cleavage site are tolerated but significantly reduce cleavage of the target RNA. With respect to the antisense strand, mismatches in the center or downstream of the cleavage site, preferably near the 3 ′ end, eg, located 1, 2, 3, 4, 5 or 6 nucleotides from the 3 ′ end of the antisense strand And shows very little reduction in target RNA cleavage.

  While not wishing to be bound by any particular theory, in some embodiments, the guide strand is at least 16 nucleotides in length and anchors the Argonaute protein in RISC. In some embodiments, when the guide strand loads into RISC, it has a well-defined seed region and cleavage of the target mRNA occurs over positions 10-11 of the guide strand. In some embodiments, the 5 'end of the guide strand is phosphorylated or can be phosphorylated. The nucleic acid molecules described herein are sometimes referred to as Minimum Length Trigger RNA.

  In some embodiments, the length of the passenger strand ranges from 8-15 nucleotides in length. In some embodiments, the passenger strand is 8, 9, 10, 11, 12, 13, 14 or 15 nucleotides in length. The passenger strand is complementary to the guide strand. Complementarity between the passenger strand and the guide strand may exist over any part of the passenger or guide strand. In some embodiments, there is 100% complementarity in the double stranded region of the molecule between the guide strand and the passenger strand.

  Aspects of the invention relate to double stranded nucleic acid molecules having a minimal double stranded region. In some embodiments, the region that is double stranded in the molecule ranges from 8-15 nucleotides in length. In some embodiments, the region that is double stranded in the molecule is 8, 9, 10, 11, 12, 13, 14, or 15 nucleotides in length. In some embodiments, the double stranded region is 13 or 14 nucleotides in length. There may be 100% complementarity between the guide strand and the passenger strand, or there may be one or more mismatches between the guide strand and the passenger strand. In some embodiments, at one end of the double-stranded molecule, the molecule is blunt ended or has a 1 nucleotide overhang. The single stranded region of the molecule is 4 to 12 nucleotides long in some embodiments. For example, the single stranded region may be 4, 5, 6, 7, 8, 9, 10, 11 or 12 nucleotides in length. However, in certain embodiments, the single stranded region may also be less than 4 nucleotides in length or greater than 12 nucleotides in length. In some embodiments, the single stranded region is at least 6 or at least 7 nucleotides in length.

  RNAi constructs related to the present invention can have a thermodynamic stability (ΔG) of less than −13 kkal / mol. In some embodiments, the thermodynamic stability (ΔG) is less than −20 kkal / mol. In some embodiments, there is a loss of efficacy when (ΔG) is less than −21 kkal / mol. In some embodiments, (ΔG) values higher than −13 kkal / mol are compatible with aspects of the invention. While not wishing to be bound by any theory, in some embodiments, molecules with relatively high (ΔG) values may become active at relatively high concentrations, while relatively Molecules with low (ΔG) values may become active at relatively low concentrations. In some embodiments, the (ΔG) value may be higher than −9 kkcal / mol. The gene silencing effect mediated by the RNAi constructs related to the present invention with minimal double stranded regions is unpredictable. This is because molecules of nearly identical design but less thermodynamic stability have been shown to be inactive (Rana et al. 2004).

  Without wishing to be bound by any theory, the results described herein show that an 8-10 bp extension of dsRNA or dsDNA is structurally recognized by a protein that is a component of RISC or a cofactor of RISC Suggest that it will be done. Furthermore, free for triggering compounds that can be perceived by protein components and / or that are sufficiently stable to interact with such components and can therefore be loaded into an Argonaute protein. There is an energy demand. Duplexes are recognized and loaded into the RNAi machinery when there is optimal thermodynamics, preferably a double stranded portion that is at least 8 nucleotides.

  In some embodiments, thermodynamic stability is increased through the use of LNA bases. In some embodiments, additional chemical modifications are introduced. Examples of some non-limiting chemical modifications include 5 ′ phosphate, 2′-O-methyl, 2′-O-ethyl, 2′-fluoro, ribothymidine, C-5 propynyl-dC (pdC) and C— 5-propynyl-dU (pdU); C-5 propynyl-C (pC) and C-5 propynyl-U (pU); 5-methyl C, 5-methyl U, 5-methyl dC, 5-methyl dU methoxy, ( 2,6-diaminopurine), 5'-dimethoxytrityl-N4-ethyl-2'-deoxycytidine and MGB (minor groove binder). It should be understood that more than one chemical modification may be combined within the same molecule.

  Molecules related to the present invention are optimized for increased potency and / or reduced toxicity. For example, the nucleotide length of the guide and / or passenger strand, and / or the number of phosphorothioate modifications in the guide and / or passenger strand, in some aspects, affects the potency of the RNA molecule, while 2′− Replacing fluoro (2′F) modifications with 2′-O-methyl (2′OMe) modifications, in some aspects, affects the toxicity of the molecule. Specifically, a decrease in the 2'F content of a molecule is expected to reduce the toxicity of the molecule. The example section presents molecules in which the 2'F modification has been removed, providing benefits due to the expected reduction in toxicity to the previously described RNAi compounds. Furthermore, the number of phosphorothioate modifications in an RNA molecule can affect the efficiency of molecular uptake into cells, eg, passive uptake of molecules into cells. Preferred embodiments of the molecules described herein do not have 2'F modifications and are still characterized by equivalent potency in cellular uptake and tissue penetration. Such molecules represent a significant improvement over the prior art, such as those described by Accell and Wolfrum, which are heavily modified by extensive use of 2'F.

  In some embodiments, the guide strand is about 18-19 nucleotides in length and has about 2-14 phosphate modifications. For example, the guide strand may comprise more than 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 or 14 nucleotides that are phosphate modified. The guide strand may include one or more modifications that increase stability without interfering with RISC entry. Phosphate modified nucleotides, such as phosphorothioate modified nucleotides, may be at the 3 'end, at the 5' end, or may extend throughout the guide strand. In some embodiments, the 10 nucleotides at the 3 'end of the guide strand comprise 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 phosphorothioate modified nucleotides. The guide strand may also include 2'F and / or 2'OMe modifications, which may be located throughout the molecule. In some embodiments, the nucleotide at position 1 of the guide strand (the nucleotide at the 5'-most position of the guide strand) is 2'OMe modified and / or phosphorylated. C and U nucleotides in the guide strand may be 2'F modified. For example, the C and U nucleotides at positions 2-10 of the 19 nt guide strand (or corresponding positions in different length strands) may be 2'F modified. C and U nucleotides in the guide strand may also be 'OMe modified. For example, the C and U nucleotides at positions 11-18 of the 19 nt guide strand (or corresponding positions in different length strands) may be 2'OMe modified. In some embodiments, the nucleotide at the most 3 'end of the guide strand is unmodified. In certain embodiments, the majority of C and U in the guide strand is 2'F modified and the 5 'end of the guide strand is phosphorylated. In other embodiments, C or U at positions 1 and 11-18 is 2'OMe modified and the 5 'end of the guide strand is phosphorylated. In other embodiments, C or U at positions 1 and 11-18 is 2′OMe modified, the 5 ′ end of the guide strand is phosphorylated, and C or U at positions 2-10 is 2 'F-modified.

  In some aspects, the optimal passenger strand is about 11-14 nucleotides in length. The passenger strand may contain modifications that increase stability. One or more nucleotides in the passenger strand may be 2'OMe modified. In some embodiments, one or more C and / or U nucleotides in the passenger strand are 2'OMe modified, or all C and U nucleotides in the passenger strand are 2'OMe modified. In certain embodiments, every nucleotide in the passenger strand is 2'OMe modified. Nucleotides 1 or more on the passenger strand may also be phosphate modified, eg phosphorothioate modified. The passenger strand may also include 2 'ribo, 2'F and 2 deoxy modifications, or any combination of the above. As shown in the examples, the chemical modification pattern in both the guide and passenger strands shows good tolerability, and a combination of chemical modifications to provide increased RNA molecule potency and self-delivery is described herein. Indicated.

  Aspects of the invention relate to RNAi constructs that have a single stranded region that is long compared to double stranded when compared to molecules previously used for RNAi. Single stranded regions of the molecule may be modified to promote cellular uptake or gene silencing. In some embodiments, phosphorothioate modification of the single stranded region affects cellular uptake and / or gene silencing. The phosphorothioate-modified region of the guide strand may include nucleotides in either the single stranded or double stranded region of the molecule. In some embodiments, the single stranded region comprises 2-12 phosphorothioate modifications. For example, the single stranded region may comprise 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or 12 phosphorothioate modifications. In some examples, the single stranded region comprises 6-8 phosphorothioate modifications.

  The molecules related to the present invention are also optimized for cellular uptake. In the RNA molecules described herein, the guide strand and / or passenger strand may be bound to a conjugate. In certain embodiments, the conjugate is hydrophobic. The hydrophobic conjugate may be a small molecule having a partition coefficient higher than 10. The conjugate may be a sterol-type molecule such as cholesterol or a molecule having an increased length polycarbon chain attached to C17, the presence of the conjugate in the presence of a lipid transfection reagent. Or it can affect the ability of RNA molecules to be taken up by cells in the absence. The conjugate may be attached to the passenger strand or guide strand through a hydrophobic linker. In some embodiments, the hydrophobic linker is 5-12C long and / or is based on hydroxypyrrolidine. In some embodiments, the hydrophobic conjugate binds to the passenger strand and the CU residue in either the passenger strand and / or the guide strand is modified. In some embodiments, at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90% or 95% of the CU residues of the passenger strand and / or guide strand are It is qualified. In some aspects, the molecules related to the present invention are self-delivering (sd). As used herein, “self-delivery” refers to the ability of a molecule to be delivered to a cell without the need for an additional delivery vehicle such as a transfection reagent.

  Aspects of the invention relate to selecting molecules for use in RNAi. In some embodiments, molecules having a double-stranded region of 8-15 nucleotides can be selected for use in RNAi. In some embodiments, the molecule is selected based on its thermodynamic stability (ΔG). In some embodiments, molecules with (ΔG) less than −13 kkal / mol are selected. For example, the (ΔG) value may be less than −13, −14, −15, −16, −17, −18, −19, −21, −22, or −22 kkal / mol. In other embodiments, the (ΔG) value may be higher than −13 kkal / mol. For example, the (ΔG) value may be higher than -12, -11, -10, -9, -8, -7, or -7 kkal / mol. It should be understood that ΔG can be calculated using any method known in the art. In some embodiments, ΔG is calculated using Mfold available through the Mfold internet site (mfold.bioinfo.rpi.edu/cgi-bin/rna-form1.cgi). Methods for calculating ΔG are described in and incorporated by reference in the following references: Zuker, M. (2003) Nucleic Acid Res., 31 (13): 3406-15; Mathews, DH, Sabina , J., Zuker, M. and Turner, DH (1999) J. Mol. Biol. 288: 911-940; Mathews, DH, Disney, MD, Childs, JL, Schroeder, SJ, Zuker, M., and Turner , DH (2004) Proc. Natl. Acad. Sci. 101: 7287-7292; Duan, S., Mathews, DH, and Turner, DH (2006) Biochemistry 45: 9819-9832; Wuchty, S., Fontana, W ., Hofacker, IL, and Schuster, P. (1999) Biopolymers 49: 145-165.

  In certain embodiments, the polynucleotide comprises 5'- and / or 3'-terminal overhangs. The number and / or sequence of nucleotide overhangs at one end of the polynucleotide may be the same or different from the other end of the polynucleotide. In certain embodiments, one or more of the overhanging nucleotides may include chemical modifications such as phosphorothioate or 2'-OMe modifications.

  In certain embodiments, the polynucleotide is unmodified. In other embodiments, at least one nucleotide is modified. In a further embodiment, the modification comprises a 2'-H or 2'-modified ribose sugar at the second nucleotide from the 5 'end of the guide sequence. The “second nucleotide” is defined as the second nucleotide from the 5 ′ end of the polynucleotide.

  As used herein, “2′-modified ribose sugar” includes ribose sugars that do not have a 2′-OH group. A “2′-modified ribose sugar” does not include 2′-deoxyribose (found in an unmodified reference DNA nucleotide). For example, the 2'-modified ribose sugar may be 2'-O-alkyl nucleotides, 2'-deoxy-2'-fluoro nucleotides, 2'-deoxy nucleotides, or combinations thereof.

  In some embodiments, the 2'-modified nucleotide is a pyrimidine nucleotide (eg, C / U). Examples of 2'-O-alkyl nucleotides include 2'-O-methyl nucleotides or 2'-O-allyl nucleotides.

  In certain embodiments, an sd-rxRNA polynucleotide of the invention having a 5 ′ end modification as described above is significantly (eg, at least about 25% when compared to a similar construct without the specified 5 ′ end modification. 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90% or more) It represents “off-target” gene silencing and thus significantly improves the overall specificity of the RNAi reagent or therapy.

As used herein, “off-target” gene silencing refers to unintended gene silencing, for example due to false sequence homology between an antisense (guide) sequence and an unintended target mRNA sequence. Refers to Thing.
In accordance with this aspect of the present invention, certain guide strand modifications do not significantly reduce RNAi activity (or do not reduce RNAi activity at all), further increase nuclease stability and / or enhance interferon induction. Reduce.

  In some embodiments, the 5 ′ stem sequence comprises a 2′-modified ribose sugar, such as a 2′-O-methyl modified nucleotide at the second nucleotide at the 5 ′ end of the polynucleotide, In this embodiment, no other modified nucleotides are contained. Hairpin structures with modifications may enhance target specificity or reduce off-target silencing compared to similar constructs that do not have 2'-O-methyl modifications in one of the above.

  Specific combinations of specific 5 ′ stem sequence modifications and 3 ′ stem sequence modifications may be partially due to increased ability to inhibit target gene expression, increased serum stability, and / or increased target specificity, etc. Can bring about additional unexpected benefits that are expressed in the

  In certain embodiments, the guide strand comprises a 2'-O-methyl modified nucleotide at the second nucleotide at the 5 'end of the guide strand or no other modified nucleotides.

  In other aspects, the sd-rxRNA structures of the present invention mediate sequence-dependent gene silencing by a microRNA mechanism. As used herein, the term “microRNA” (“miRNA”) is also referred to in the art as “small temporal RNA” (“stRNA”) and is genetically (eg, Refers to small (10-50 nucleotides) RNA encoded by a virus, mammal or plant genome that can direct or mediate RNA silencing. “MiRNA disorder” should refer to a disease or disorder characterized by aberrant expression or activity of miRNA.

  MicroRNAs are involved in down-regulating target genes in important pathways such as development or cancer in mice, insects and mammals. Gene silencing through the microRNA mechanism is achieved by base pairing between a specific but still incomplete miRNA and its target messenger RNA (mRNA). A variety of mechanisms can be used in microRNA-mediated down-regulation of target mRNA expression.

  miRNAs are non-coding RNAs of about 22 nucleotides that can regulate gene expression at the post-transcriptional or translational level during plant and animal development. One common feature of miRNAs is that they are excised from an approximately 70 nucleotide precursor RNA stem loop called pre-miRNA, presumably by Dicer or its homologue, an RNase type III enzyme. is there. Naturally occurring miRNAs are expressed in vivo by endogenous genes and processed from hairpins or stem-loop precursors (pre-miRNAs or pri-miRNAs) by dicers or other RNAse. miRNAs can exist transiently as a double-stranded duplex in vivo, but only one strand is incorporated into the RISC complex to direct gene silencing.

  In some embodiments, versions of sd-rxRNA compounds that are effective in cellular uptake and miRNA inhibition are described. In essence, the compound is similar to the RISC invasive version, but optimized so that the chemical modification pattern of the large chain blocks the cleavage and acts as an effective effective inhibitor of RISC action. Yes. For example, the compound may be fully or almost O-methyl modified with the PS content described above. For these types of compounds, 5 'phosphorylation is not necessary. The presence of the double stranded region is preferred as it promotes cellular uptake and efficient RISC loading.

  Another pathway that uses small RNAs as sequence-specific regulators is the RNA interference (RNAi) pathway, which is an evolutionarily conserved response to the presence of double-stranded RNA (dsRNA) in cells. dsRNA is cleaved by Dicer into small interfering RNA (siRNA) of about 20 base pairs (bp) duplex. These small RNAs are assembled into a multiprotein effector complex called the RNA-induced silencing complex (RISC). The siRNA then guides the cleavage of the target mRNA with perfect complementarity.

  Some aspects of biogenesis, protein complexes and function are shared between the siRNA and miRNA pathways. The single-stranded polynucleotide of interest mimics dsRNA in the siRNA mechanism or mimics microRNA in the miRNA mechanism.

In certain embodiments, a modified RNAi construct may have improved serum and / or cerebrospinal fluid stability compared to an unmodified RNAi construct having the same sequence.
In certain embodiments, the structure of the RNAi construct does not induce an interferon response in primary cells, such as mammalian primary cells, including primary cells from humans, mice and other rodents, and other non-human mammals. In certain embodiments, RNAi constructs can also be used to inhibit target gene expression in invertebrate organisms.

  In order to further increase the in vivo stability of the construct of interest, the 3 'end of the hairpin structure may be blocked with a protecting group. For example, protecting groups such as inverted nucleotides, inverted abasic moieties, or amine O-modified nucleotides can be used. Inverted nucleotides may include inverted deoxynucleotides. The inverted abasic moiety may comprise an inverted deoxyabasic moiety, such as a 3 ', 3' bond or a 5 ', 5' linked deoxyabasic moiety.

  The RNAi construct of the present invention can inhibit the synthesis of any target protein encoded by the target gene. The present invention includes a method of inhibiting expression of a target gene in a cell, either in vitro or in vivo. Thus, the RNAi constructs of the present invention are useful for treating patients with diseases characterized by overexpression of the target gene.

  The target gene may be endogenous to the cell or exogenous (eg, introduced into the cell by a virus or using recombinant DNA technology). Such methods may include the introduction of RNA into the cell in an amount sufficient to inhibit expression of the target gene. For example, such RNA molecules include a guide strand that is complementary to the nucleotide sequence of the target gene such that the composition inhibits expression of the target gene.

The invention also relates to vectors that express the nucleic acids of the invention and cells containing such vectors or nucleic acids. The cell may be a mammalian cell, such as a human cell, in vivo or in culture.
The mammal further relates to a composition comprising the RNAi construct of interest and a pharmaceutically acceptable carrier or diluent.

Another aspect of the invention provides a method for inhibiting the expression of a target gene in a mammalian cell, the method comprising contacting an ocular cell with any of the RNAi constructs of interest. including.
The method can be performed in vitro, ex vivo, or in vivo, eg, in a mammalian cell in culture, such as a human cell in culture.
Target cells (eg, mammalian cells) may be contacted in the presence of delivery reagents such as lipids (eg, cationic lipids) or liposomes.
Another aspect of the invention provides a method for inhibiting the expression of a target gene in a mammalian cell, the method comprising contacting the mammalian cell with a vector that expresses the RNAi construct of interest. .

  In one aspect of the invention, a longer duplex comprising a first polynucleotide having a size in the range of about 16 to about 30 nucleotides and a second polynucleotide having a size in the range of about 26 to about 46 nucleotides. A polynucleotide is provided, wherein the first polynucleotide (antisense strand) is complementary to both the second polynucleotide (sense strand) and the target gene, wherein both polynucleotides are Forming a duplex, wherein the first polynucleotide comprises a single stranded region longer than 6 bases in length, has been modified by an alternative chemical modification pattern, and / or Conjugate moieties that facilitate cell delivery are included. In this embodiment, about 40 to about 90% of the nucleotides of the passenger strand, about 40 to about 90% of the nucleotides of the guide strand, and about 40 to about 90% of the nucleotides of the single-stranded region of the first polynucleotide are chemically It is a modified nucleotide.

  In one aspect, the chemically modified nucleotides in the polynucleotide duplex may be any chemically modified nucleotide known in the art, such as those discussed in detail above. In certain embodiments, the chemically modified nucleotide is selected from the group consisting of 2'F modified nucleotides, 2'-O-methyl modified and 2'deoxy nucleotides. In another specific embodiment, the chemically modified nucleotide results from a “hydrophobic modification” of the nucleotide base. In another specific embodiment, the chemically modified nucleotide is phosphorothioate. In yet another specific embodiment, the chemically modified nucleotide is a combination of phosphorothioate, 2'-O-methyl, 2'deoxy, hydrophobic modification and phosphorothioate. Where these groups of modifications refer to ribose ring, backbone and nucleotide modifications, some modified nucleotides may include combinations of all three types of modifications.

  In another embodiment, the chemical modification is not the same across the various regions of the duplex. In certain embodiments, the first polynucleotide (passenger strand) has a number of diverse chemical modifications at various positions. For this polynucleotide, up to 90% of the nucleotides may be chemically modified and / or have introduced mismatches.

In another embodiment, chemical modifications of the first or second polynucleotide include, but are not limited to, modifications of uridine and cytosine at the 5 ′ position (4-pyridyl, 2-pyridyl, indolyl, phenyl (C ₆ H ₅ OH ); Tryptophanyl (C8H6N) CH2CH (NH2) CO), isobutyl, butyl, aminobenzyl; phenyl; naphthyl, etc.), where chemical modification may alter the base pairing ability of the nucleotide. For the guide strand, an important feature of this aspect of the invention is the position and sequence of chemical modification to the 5 ′ end of the antisense. For example, chemical phosphorylation of the 5 ′ end of the guide strand is usually beneficial for efficacy. O-methyl modifications in the seed region of the sense strand (positions 2-7 relative to the 5 'end) generally do not show good tolerability, whereas 2'F and deoxy show good tolerability . The middle part of the guide strand and the 3 ′ end of the guide strand are more permissive in the type of chemical modification applied. Deoxy modification is not tolerated at the 3 'end of the guide strand.

A unique feature of this aspect of the invention involves the use of hydrophobic modifications to the base. In one aspect of the invention, the hydrophobic modifications are preferably located near the 5 ′ end of the guide strand, in other embodiments they are located in the middle of the guide strand, and in other embodiments they are Are located at the 3 ′ end of the guide strand, and in yet another embodiment they are distributed throughout the length of the polynucleotide. The same type of pattern can be applied to the duplex passenger strand.
The other part of the molecule is a single stranded region. The single stranded region is predicted to be in the range of 7-40 nucleotides.

  In one aspect, the single-stranded region of the first polynucleotide comprises 40% to 90% hydrophobic base modification, 40% to 90% phosphorothioate, 40% to 90% ribose moiety modification, and A modification selected from the group consisting of any combination is included.

In one embodiment of the invention, the efficiency of loading the guide strand (first polynucleotide) into the RISC complex may vary for heavily modified polynucleotides. To facilitate loading, the duplex polynucleotide comprises nucleotides 9, 11, 12, 13 or 14 on the guide strand (first polynucleotide) and the opposite nucleotide on the sense strand (second polynucleotide). Including a mismatch between
More detailed aspects of the invention are described in the following sections.

Duplex Features The double-stranded oligonucleotides of the present invention can be formed by two separate complementary nucleic acid strands. Duplex formation may occur inside or outside the cell containing the target gene.

  As used herein, the term “duplex” includes a region of a double-stranded nucleic acid molecule that is hydrogen bonded to a complementary sequence. The double-stranded oligonucleotides of the present invention can include a nucleotide sequence that is sense to the target gene and a complementary sequence that is antisense to the target gene. The sense and antisense nucleotide sequences correspond to the target gene sequence and are, for example, identical to the target gene sequence or sufficiently identical to result in inhibition of the target gene (eg, approximately at least about 98% identical, 96% Identical, 94%, 90% identical, 85% identical or 80% identical).

  In certain embodiments, a double-stranded oligonucleotide of the invention is double-stranded over its entire length, ie, has no single-stranded sequence protruding at either end of the molecule, ie, is blunt ended. In other embodiments, individual nucleic acid molecules may be of different lengths. In other words, the double-stranded oligonucleotide of the present invention is not double-stranded over its entire length. For example, if two separate nucleic acid molecules are used, one of the molecules, eg, a first molecule containing an antisense sequence, may be longer than a second molecule that hybridizes to it (one portion of the molecule A chain). Similarly, if a single nucleic acid molecule is used, any end portion of the molecule may remain single stranded.

  In one embodiment, the double stranded oligonucleotide of the invention comprises a mismatch and / or a loop or bulge, but is double stranded over at least about 70% of the length of the oligonucleotide. In another embodiment, the double stranded oligonucleotide of the invention is double stranded over at least about 80% of the length of the oligonucleotide. In another embodiment, the double stranded oligonucleotide of the invention is double stranded over at least about 90% to 95% of the length of the oligonucleotide. In another embodiment, the double-stranded oligonucleotide of the invention is double-stranded over at least about 96% to 98% of the length of the oligonucleotide. In certain embodiments, the double-stranded oligonucleotide of the invention comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 or 15 mismatches. .

Modifications The nucleotides of the invention can be modified at a variety of positions, including sugar moieties, phosphodiester linkages and / or bases.

  In some embodiments, the base portion of the nucleoside may be modified. For example, the pyrimidine base may be modified at the 2, 3, 4, 5, and / or 6 position of the pyrimidine ring. In some embodiments, the exocyclic amine of cytosine may be modified. Purine bases may also be modified. For example, the purine base may be modified at positions 1, 2, 3, 6, 7, or 8. In some embodiments, the exocyclic amine of adenine may be modified. In some cases, the nitrogen atom in the ring of the base moiety may be substituted with another atom such as carbon. The modification to the base moiety may be any suitable modification. Examples of modifications are known to those skilled in the art. In some embodiments, base modifications include alkylated purines or pyrimidines, acylated purines or pyrimidines or other heterocycles.

In some embodiments, the pyrimidine may be modified at the 5 position. For example, the 5-position of pyrimidine may be modified with an alkyl group, an alkynyl group, an alkenyl group, an acyl group, or a substituted derivative thereof. In other examples, the 5-position of the pyrimidine may be modified with a hydroxyl group or an alkoxyl group or substituted derivatives thereof. In addition, the N ⁴ position of pyrimidine may be alkylated. In yet another example, the 5-6 bond of the pyrimidine may be saturated, the nitrogen atom in the pyrimidine ring may be substituted with a carbon atom, and / or the O ² and O ⁴ atoms are sulfur atoms. May be substituted. It should be understood that other modifications are also possible.

In another example, N ^7-position of the purine and / or N ² and / or N ^3-position may be modified with an alkyl group or substituted derivatives thereof. In a further example, the third ring may be fused to the purine bicyclic ring system and / or the nitrogen atom in the purine ring system may be substituted by a carbon atom. It should be understood that other modifications are also possible.

Non-limiting examples of pyrimidines modified at position 5 are disclosed in US Pat. No. 5,591,843, US Pat. No. 7,205,297, US Pat. No. 6,432,963 and US Pat. No. 6,020,483; pyrimidines modified at position N ⁴ Non-limiting examples of are disclosed in US Pat. No. 5,580,731; non-limiting examples of purines modified at position 8 are disclosed in US Pat. No. 6,355,787 and US Pat. No. 5,580,972; position N ⁶ Non-limiting examples of purines modified in are disclosed in US Pat. No. 4,853,386, US Pat. No. 5,789,416, and US Pat. No. 7,041,824; and non-limiting examples of purines modified in position 2 Are disclosed in US Pat. No. 4,201,860 and US Pat. No. 5,587,469, all of which are incorporated herein by reference.

Non-limiting examples of modified ^bases, N 4, ^{N 4} - Etanoshitoshin, 7 der Zaki Santo Singh, 7- deazaguanosine, 8-oxo -N ⁶ - methyl adenine, 4-acetyl cytosine, 5- (Carboxyhydroxylmethyl) uracil, 5-fluorouracil, 5-bromouracil, 5-carboxymethylaminomethyl-2-thiouracil, 5-carboxymethylaminomethyluracil, dihydrouracil, inosine, N ⁶ -isopentenyl-adenine, 1- Methyladenine, 1-methylpseudouracil, 1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3-methylcytosine, 5-methylcytosine, N ⁶ -methyladenine, 7-methylguanine, 5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil, 5-methoxyuracil, 2-methylthio-N ⁶ -isopentenyladenine, pseudouracil, 5-methyl-2-thiouracil, 2-thiouracil, 4- Examples include thiouracil, 5-methyluracil, 2-thiocytosine, and 2,6-diaminopurine. In some embodiments, the base moiety may be a heterocyclic base other than purine or pyrimidine. The heterocyclic base may be optionally modified and / or substituted.

  Sugar moieties include natural unmodified sugars, such as monosaccharides (pentoses such as ribose, deoxyribose, etc.), modified sugars and sugar analogs. In general, possible nucleomonomer modifications, particularly for sugar moieties, such as replacement of one or more of the hydroxyl groups with halogens, heteroatoms, aliphatic groups, or hydroxyl groups of ethers, amines, thiols, etc. As functionalization.

  One particularly useful group of modified nucleomonomers is 2'-O-methyl nucleotides. Such 2′-O-methyl nucleotides may be referred to as “methylated” and the corresponding nucleotides are made from unmethylated nucleotides by alkylation or directly from methylated nucleotide reagents. It is done. The modified nucleomonomer may be used in combination with an unmodified nucleomonomer. For example, the oligonucleotides of the invention may include both methylated and unmethylated nucleomonomers.

Some exemplary modified nucleomonomers include sugars or backbone modified ribonucleotides. Modified ribonucleotides include uridine or cytidine modified at the 5 ′ position, such as 5 ′-(2-amino) propyl uridine and 5′-bromouridine; adenosine and guanosine modified at the 8 position, such as 8-bromoguanosine; Non-naturally occurring bases (instead of naturally occurring bases) such as deazanucleotides, such as 7-deaza-adenosine; and N-alkylated nucleotides, such as N6-methyladenosine, may also be included. Also, sugar-modified ribonucleotides, H, alkoxy (or OR), R or alkyl, halogen, SH, SR, amino _(NH 2, NHR, NR _2, etc.) 2'-OH group has been replaced by, or CN group Where R is lower alkyl, alkenyl or alkynyl.

  Modified ribonucleotides may also have phosphodiester groups linked to adjacent ribonucleotides that are replaced by modifying groups, such as phosphorothioate groups. More generally, various nucleotide modifications may be combined.

  Although the antisense (guide) strand can be substantially identical to at least a portion of the target gene, at least in relation to base pairing, the sequence can be useful, for example, a phenotype of the target gene. It is not necessary for the expression to be completely identical. In general, higher homology can be used to compensate for the use of shorter antisense genes. In some cases, the antisense strand is generally substantially identical (in the antisense direction) to the target gene.

  The use of 2'-O-methyl modified RNA may also be beneficial in situations where it is desirable to minimize the cellular stress response. RNA with 2'-O-methyl nucleomonomers cannot be recognized by cellular mechanisms that are thought to recognize unmodified RNA. RNA that is 2'-O-methylated or partially 2'-O-methylated can avoid interferon responses to double-stranded nucleic acids while maintaining target RNA inhibition. This is useful, for example, in both short RNAi (eg siRNA) sequences that induce an interferon response and longer RNAi sequences that can induce an interferon response to avoid interferon or other cellular stress responses. obtain.

Overall, as modified sugars, D-ribose, 2′-O-alkyl (including 2′-O-methyl and 2′-O-ethyl), ie 2′-alkoxy, 2′-amino, 2′- S-alkyl, 2′-halo (including 2′-fluoro), 2′-methoxyethoxy, 2′-allyloxy (—OCH ₂ CH═CH ₂ ), 2′-propargyl, 2′-propyl, ethynyl, ethenyl , Propenyl, cyano and the like. In one embodiment, the sugar moiety may be hexose as described (Augustyns, K., et al., Nucl. Acids. Res. 18: 4711 (1992)) and incorporated into the oligonucleotide. May be. Exemplary nucleomonomers can be found, for example, in US Pat. No. 5,849,902, which is incorporated herein by reference.

  Definitions of specific functional groups and chemical terms are described in more detail below. For the purposes of the present invention, chemical elements are identified according to the periodic table of elements, CAS version, Handbook of Chemistry and Physics, internal cover of the 75th edition, and specific functional groups are generally defined therein It is as follows. In addition, the general principles of organic chemistry, as well as specific functional moieties and reactivity, are described in Organic Chemistry, Thomas Sorrell, University Science Books, Sausalito (1999), the entire contents of which are hereby incorporated by reference. Incorporated.

  Certain compounds of the present invention may exist in particular geometric or stereoisomeric forms. The present invention includes cis- and trans-isomers, R- and S-enantiomers, diastereomers, (D) -isomers, (L) -isomers, their racemic mixtures, and other mixtures thereof All such compounds are contemplated as falling within the scope of the present invention. Additional asymmetric carbon atoms may be present in a substituent such as an alkyl group. All such isomers as well as mixtures thereof are intended to be included in the present invention.

  Isomeric mixtures, including those of all various isomer ratios, can be utilized according to the present invention. For example, when only two isomers are combined, 50:50, 60:40, 70:30, 80:20, 90:10, 95: 5, 96: 4, 97: 3, 98: 2, 99 All mixtures containing isomer ratios of 1: 1, or 100: 0 are contemplated by the present invention. One skilled in the art will readily appreciate that similar ratios are contemplated for more complex isomer mixtures.

  For example, if a particular enantiomer of a compound of the invention is desired, it can be prepared by asymmetric synthesis or by derivatization with a chiral auxiliary, where the resulting diastereomeric mixture is Separate and cleave the auxiliary group to give the pure desired enantiomer. Alternatively, if the molecule contains a basic functional group such as amino or an acidic functional group such as carboxyl, a diastereomeric salt is formed with a suitable optically active acid or base, and then the formed diastereomers are Resolution by fractional recrystallization or chromatographic methods well known in the art, after which the pure enantiomer is recovered.

In certain embodiments, the oligonucleotides of the invention include 3 ′ and 5 ′ ends (excluding circular oligonucleotides). In one embodiment, the 3 ′ and 5 ′ ends of the oligonucleotide are substantially protected from nucleases, eg, by modifying the 3 ′ or 5 ′ linkage (eg, US Pat. No. 5,849,902 and WO 98/13526). It may be. For example, oligonucleotides can be made resistant by the inclusion of “blocking groups”. The term “blocking group” as used herein refers to a substituent (eg, other than an OH group) that can be attached to an oligonucleotide or nucleomonomer as either a protecting group or a coupling group for synthesis. (Eg, FITC, propyl (CH ₂ —CH ₂ —CH ₃ ), glycol (—O—CH ₂ —CH ₂ —O—) phosphonate (PO ₃ ²⁻ ), hydrogen phosphonate) Or phosphoramidites). “Blocking groups” also include “end blocking groups” or “exonuclease blocking groups” that protect the 5 ′ and 3 ′ ends of oligonucleotides including modified nucleotides and non-nucleotide exonuclease resistant structures.

  Exemplary endblocking groups include cap structures (eg, 7-methylguanosine cap), inverted nucleomonomers, eg, by inversion of the 3′-3 ′ or 5′-5 ′ end (eg, Ortiagao et al. 1992. Antisence Res. Dev. 2: 129), methylphosphonates, phosphoramidites, non-nucleotide groups (eg, non-nucleotide linkers, amino linkers, conjugates) and the like. The 3 'terminal nucleomonomer may comprise a modified sugar moiety. The 3 'terminal nucleomonomer includes 3'-O, which may optionally be substituted with a blocking group that prevents 3'-exonuclease degradation of the oligonucleotide. For example, the 3'-hydroxyl may be esterified to the nucleotide through a 3 '→ 3' internucleotide linkage. For example, the alkyloxy radical may be methoxy, ethoxy or isopropoxy, preferably ethoxy. Optionally, the 3 ′ → 3 ′ linked nucleotide at the 3 ′ end may be linked by a substitution bond. In order to reduce nuclease degradation, a 5 ′ most 3 ′ → 5 ′ linkage is a modified linkage, such as a phosphorothioate or P-alkyloxyphosphotriester linkage. Also good. Preferably, the two 5 ′ most 3 ′ → 5 ′ bonds are modified bonds. Optionally, the 5'-terminal hydroxy moiety may be esterified with a phosphorus-containing moiety, a phosphorus-containing moiety such as phosphoric acid, phosphorothioate or P-ethoxyphosphoric acid.

  One skilled in the art will appreciate that the synthetic methods utilize a variety of protecting groups, as described herein. By the term “protecting group” as used herein, certain functional moieties, such as O, S, or N, are temporary so that the reaction occurs selectively at other reactive sites in the multifunctional compound. It is meant to be blocked. In some embodiments, the protecting group reacts selectively in good yields, yielding a protected substrate that is suitable for the planned reaction; the protecting group is readily available and can be used for other functional groups. Must be selectively removable in good yield with non-attacking, preferably non-toxic reagents; protecting groups can be easily separated (more preferably without creating a new asymmetric center) Form a derivative; and the protecting group has minimal additional functionality to avoid sites of further reaction.

  As detailed herein, oxygen, sulfur, nitrogen and carbon protecting groups may be utilized. As hydroxyl protecting groups, methyl, methoxylmethyl (MOM), methylthiomethyl (MTM), t-butylthiomethyl, (phenyldimethylsilyl) methoxymethyl (SMOM), benzyloxymethyl (BOM), p-methoxybenzyloxymethyl ( PMBM), (4-methoxyphenoxy) methyl (p-AOM), guaiacol methyl (GUM), t-butoxymethyl, 4-pentenyloxymethyl (POM), siloxymethyl, 2-methoxyethoxymethyl (MEM), 2, 2,2-trichloroethoxymethyl, bis (2-chloroethoxy) methyl, 2- (trimethylsilyl) ethoxymethyl (SEMOR), tetrahydropyranyl (THP), 3-bromotetrahydropyranyl, tetrahydrothiopyranyl, 1-methoxy Cyclohexyl, 4-methoxytetrahydropyranyl (MTHP 4-methoxytetrahydrothiopyranyl, 4-methoxytetrahydrothiopyranyl S, S-dioxide, 1-[(2-chloro-4-methyl) phenyl] -4-methoxypiperidin-4-yl (CTMP), 1 , 4-Dioxan-2-yl, tetrahydrofuranyl, tetrahydrofuranyl, 2,3,3a, 4,5,6,7,7a-octahydro-7,8,8-trimethyl-4,7-methanobenzofuran- 2-yl, 1-ethoxyethyl, 1- (2-chloroethoxy) ethyl, 1-methyl-1-methoxyethyl, 1-methyl-1-benzyloxyethyl, 1-methyl-1-benzyloxy-2-fluoro Ethyl, 2,2,2-trichloroethyl, 2-trimethylsilylethyl, 2- (phenylselenyl) ethyl, t-butyl, allyl, -Chlorophenyl, p-methoxyphenyl, 2,4-dinitrophenyl, benzyl, p-methoxybenzyl, 3,4-dimethoxybenzyl, o-nitrobenzyl, p-nitrobenzyl, p-halobenzyl, 2,6-dichlorobenzyl, p-cyanobenzyl, p-phenylbenzyl, 2-picolyl, 4-picolyl, 3-methyl-2-picolyl N-oxide, diphenylmethyl, p, p'-dinitrobenzhydryl, 5-dibenzosuberyl, triphenyl Methyl, α-naphthyldiphenylmethyl, p-methoxyphenyldiphenylmethyl, di (p-methoxyphenyl) phenylmethyl, tri (p-methoxyphenyl) methyl, 4- (4′-bromophenacyloxyphenyl) diphenylmethyl, 4 , 4 ', 4' '-Tris (4,5-dichloroph Ruimidophenyl) methyl, 4,4 ′, 4 ″ -tris (levulinoyloxyphenyl) methyl, 4,4 ′, 4 ″ -tris (benzoyloxyphenyl) methyl, 3- (imidazol-1-yl) ) Bis (4 ′, 4 ″ -dimethoxyphenyl) methyl, 1,1-bis (4-methoxyphenyl) -1′-pyrenylmethyl, 9-anthryl, 9- (9-phenyl) xanthenyl, 9- (9- Phenyl-10-oxo) anthryl, 1,3-benzodithiolane-2-yl, benzoisothiazolyl S, S-dioxide, trimethylsilyl (TMS), triethylsilyl (TES), triisopropylsilyl (TIPS), Dimethyl isopropyl silyl (IPDMS), diethyl isopropyl silyl (DEIPS), dimethyl texyl (thexyl) silyl, t-butyldimethyl Silyl (TBDMS), t-butyldiphenylsilyl (TBDPS), tribenzylsilyl, tri-p-xylylsilyl, triphenylsilyl, diphenylmethylsilyl (DPMS), t-butylmethoxyphenylsilyl (TBMPS), formate (formate), Benzoyl formate, acetate, chloroacetate, dichloroacetate, trichloroacetate, trifluoroacetate, methoxyacetate, triphenylmethoxyacetate, phenoxyacetate, p-chlorophenoxyacetate, 3-phenylpropionate, 4-oxopentanoate (levulinate) (Levulinate)), 4,4- (ethylenedithio) pentanoate (levulinoyl dithioacetal), pivaloate, adamantate, crotonate, 4-methoxy Crotonate, benzoate, p-phenylbenzoate, 2,4,6-trimethylbenzoate (mesitoate), alkylmethyl carbonate, 9-fluorenylmethyl carbonate (Fmoc), alkylethyl carbonate, alkyl 2,2,2-trichloroethyl carbonate (Troc), 2- (trimethylsilyl) ethyl carbonate (TMSEC), 2- (phenylsulfonyl) ethyl carbonate (Psec), 2- (triphenylphosphonio) ethyl carbonate (Peoc), alkyl isobutyl carbonate, alkyl vinyl carbonate, alkyl allyl carbonate, alkyl p-nitrophenyl carbonate, alkyl benzyl carbonate, alkyl p-methoxybenzyl carbonate, alkyl 3,4-dimethoxybenzyl carbonate Bonato, alkyl o-nitrobenzyl carbonate, alkyl p-nitrobenzyl carbonate, alkyl S-benzylthiocarbonate, 4-ethoxy-1-napthyl carbonate, methyldithiocarbonate, 2-indobenzoate, 4 Azidobutyrate, 4-nitro-4-methylpentanoate, o- (dibromomethyl) benzoate, 2-formylbenzenesulfonate, 2- (methylthiomethoxy) ethyl, 4- (methylthiomethoxy) butyrate, 2- (methylthio Methoxymethyl) benzoate, 2,6-dichloro-4-methylphenoxyacetate, 2,6-dichloro-4- (1,1,3,3-tetramethylbutyl) phenoxyacetate, 2,4-bis (1, 1-dimethylpropyl) phenoxyacete Chlorodiphenyl acetate, isobutyrate, monosuccinoate, (E) -2-methyl-2-butenoate, o- (methoxycarbonyl) benzoate, α-naphthoate, nitrate, alkyl N, N, N ′, N ′ -Tetramethyl phosphorodiamidate, alkyl N-phenylcarbamate, borate, dimethylphosphinothioyl (thioyl), alkyl 2,4-dinitrophenylsulfenate, sulfate, methanesulfonate (mesylate), benzylsulfonate, and Tosylate (Ts) is mentioned.

  In order to protect 1,2- or 1,3-diols, methylene acetal, ethylidene acetal, 1-tert-butyl ethylidene ketal, 1-phenyl ethylidene ketal, (4-methoxyphenyl) ethylidene acetal, 2,2,2-trichloroethylidene acetal, acetonide, cyclopentylidene ketal, cyclohexylidene ketal, cycloheptylidene ketal, benzylidene acetal, p-methoxybenzylidene acetal, 2,4-dimethoxybenzylidene ketal, 3,4-dimethoxy Benzylidene acetal, 2-nitrobenzylidene acetal, methoxymethylene acetal, ethoxymethylene acetal, dimethoxymethylene ortho ester, 1-methoxyethylidene ortho ester, 1-ethyl Ethoxyethylidine orthoester, 1,2-dimethoxyethylidene orthoester, α-methoxybenzylidene orthoester, 1- (N, N-dimethylamino) ethylidene derivative, α- (N, N′-dimethylamino) benzylidene derivative 2-oxacyclopentylidene orthoester, di-t-butylsilylene group (DTBS), 1,3- (1,1,3,3-tetraisopropyldisiloxanilidene) derivative (TIPDS), tetra-t- Examples include butoxydisiloxane-1,3-diylidene derivatives (TBDS), cyclic carbonates, cyclic boronates, ethyl boronate, and phenyl boronate.

  As amino protecting groups, methyl carbamate, ethyl carbamate, 9-fluorenylmethyl carbamate (Fmoc), 9- (2-sulfo) fluorenylmethyl carbamate, 9- (2,7-dibromo) fluoroenylmethyl carbamate, 2 , 7-di-t-butyl- [9- (10,10-dioxo-10,10,10,10-tetrahydrothioxanthyl)] methyl carbamate (DBD-Tmoc), 4-methoxyphenacyl carbamate (Phenoc) 2,2,2-trichloroethyl carbamate (Troc), 2-trimethylsilylethyl carbamate (Teoc), 2-phenylethyl carbamate (hZ), 1- (1-adamantyl) -1-methylethyl carbamate (Adpoc), 1 1,1-dimethyl-2-haloethylcarbamate, 1,1-dimethyl-2,2-dibro Ethyl carbamate (DB-t-BOC), 1,1-dimethyl-2,2,2-trichloroethyl carbamate (TCBOC), 1-methyl-1- (4-diphenylyl) ethyl carbamate (Bpoc), 1- (3 , 5-di-t-butylphenyl) -1-methylethylcarbamate (t-Bumeoc), 2- (2′- and 4′-pyridyl) ethylcarbamate (Pyoc), 2- (N, N-dicyclohexylcarboxamide) Ethyl carbamate, t-butyl carbamate (BOC), 1-adamantyl carbamate (Adoc), vinyl carbamate (Voc), allyl carbamate (Alloc), 1-isopropyl allyl carbamate (Ipaoc), cinnamyl carbamate (Coc), 4-nitro Cinnamyl carbamate (Noc), 8-quinolyl carbamate, N-hydroxypiperidinyl carbamate, Rualkyldithiocarbamate, benzylcarbamate (Cbz), p-methoxybenzylcarbamate (Moz), p-nitobenzylcarbamate, p-bromobenzylcarbamate, p-chlorobenzylcarbamate, 2,4-dichlorobenzylcarbamate, 4-methyl Sulfinyl benzyl carbamate (Msz), 9-anthrylmethyl carbamate, diphenylmethyl carbamate, 2-methylthioethyl carbamate, 2-methylsulfonylethyl carbamate, 2- (p-toluenesulfonyl) ethyl carbamate, [2- (1,3- Dithianyl)] methyl carbamate (Dmoc), 4-methylthiophenyl carbamate (Mtpc), 2,4-dimethylthiophenyl carbamate (Bmpc), 2-phosphonioethyl carbamate (Peoc), 2 -Triphenylphosphonioisopropyl carbamate (Ppoc), 1,1-dimethyl-2-cyanoethyl carbamate, m-chloro-p-acyloxybenzyl carbamate, p- (dihydroxyboryl) benzyl carbamate, 5-benzoisoxazolyl methyl carbamate 2- (trifluoromethyl) -6-chromonylmethyl carbamate (Tcroc), m-nitrophenyl carbamate, 3,5-dimethoxybenzyl carbamate, o-nitrobenzyl carbamate, 3,4-dimethoxy-6-nitrobenzyl carbamate Phenyl (o-nitrophenyl) methylcarbamate, phenothiazinyl- (10) -carbonyl derivative, N′-p-toluenesulfonylaminocarbonyl derivative, N′-phenylaminothiocarbonyl derivative, t Amylcarbamate, S-benzylthiocarbamate, p-cyanobenzylcarbamate, cyclobutylcarbamate, cyclohexylcarbamate, cyclopentylcarbamate, cyclopropylmethylcarbamate, p-decyloxybenzylcarbamate, 2,2-dimethoxycarbonylvinylcarbamate, o- (N , N-dimethylcarboxamide) benzylcarbamate, 1,1-dimethyl-3- (N, N-dimethylcarboxamido) propylcarbamate, 1,1-dimethylpropynylcarbamate, di (2-pyridyl) methylcarbamate, 2-furanylmethyl Carbamate, 2-iodoethyl carbamate, isoborynl carbamate, isobutyl carbamate, isonicotinyl carbamate, p- (p′-me Xylphenylazo) benzylcarbamate, 1-methylcyclobutylcarbamate, 1-methylcyclohexylcarbamate, 1-methyl-1-cyclopropylmethylcarbamate, 1-methyl-1- (3,5-dimethoxyphenyl) ethylcarbamate, 1- Methyl-1- (p-phenylazophenyl) ethylcarbamate, 1-methyl-1-phenylethylcarbamate, 1-methyl-1- (4-pyridyl) ethylcarbamate, phenylcarbamate, p- (phenylazo) benzylcarbamate, 2 , 4,6-tri-t-butylphenylcarbamate, 4- (trimethylammonium) benzylcarbamate, 2,4,6-trimethylbenzylcarbamate, formamide, acetamide, chloroacetamide, trichloroacetamide, Trifluoroacetamide, phenylacetamide, 3-phenylpropanamide, picolinamide, 3-pyridylcarboxamide, N-benzoylphenylalanyl derivative, benzamide, p-phenylbenzamide, o-nitrophenylacetamide, o-nitro Phenoxyacetamide, acetoacetamide, (N′-dithiobenzyloxycarbonylamino) acetamide, 3- (p-hydroxyphenyl) propanamide, 3- (o-nitrophenyl) propanamide, 2-methyl-2- (o- Nitrophenoxy) propanamide, 2-methyl-2- (o-phenylazophenoxy) propanamide, 4-chlorobutanamide, 3-methyl-3-nitrobutanamide, o-nitrocinnamide, N-acetylmethionine derivative, o- Nitrobenza O- (benzoyloxymethyl) benzamide, 4,5-diphenyl-3-oxazolin-2-one, N-phthalimide, N-dithiasuccinimide (Dts), N-2,3-diphenylmaleimide, N-2 , 5-dimethylpyrrole, N-1,1,4,4-tetramethyldisilylazacyclopentane adduct (STABASE), 5-substituted 1,3-dimethyl-1,3,5-triazacyclohexane 2-one, 5-substituted 1,3-dibenzyl-1,3,5-triazacyclohexane-2-one, 1-substituted 3,5-dinitro-4-pyridone, N-methylamine, N-allylamine, N- [2- (trimethylsilyl) ethoxy] methylamine (SEM), N-3-acetoxypropylamine, N- (1-isopropyl-4-nitro-2-oxo-3-pyro N-3-yl) amine, quaternary ammonium salt, N-benzylamine, N-di (4-methoxyphenyl) methylamine, N-5-dibenzosuberylamine, N-triphenylmethylamine (Tr), N- [(4-Methoxyphenyl) diphenylmethyl] amine (MMTr), N-9-phenylfluorenylamine (PhF), N-2,7-dichloro-9-fluorenylmethyleneamine, N-ferrocenylmethylamino (Fcm), N-2-picolylamino N′-oxide, N-1,1-dimethylthiomethyleneamine, N-benzylideneamine, Np-methoxybenzylideneamine, N-diphenylmethyleneamine, N-[(2- Pyridyl) mesityl] methyleneamine, N- (N ′, N′-dimethylaminomethylene) amine, N, N′-isopropylidenedia N-p-nitrobenzylideneamine, N-salicylideneamine, N-5-chlorosalicylideneamine, N- (5-chloro-2-hydroxyphenyl) phenylmethyleneamine, N-cyclohexylideneamine, N- (5,5-dimethyl-3-oxo-1-cyclohexenyl) amine, N-borane derivative, N-diphenylborinic acid derivative, N- [phenyl (pentacarbonylchromium- or tungsten) carbonyl] amine, N- Copper chelate, N-zinc chelate, N-nitroamine, N-nitrosamine, amine N-oxide, diphenylphosphinamide (Dpp), dimethylthiophosphineamide (Mpt), diphenylthiophosphineamide (Ppt), dialkyl phosphoramidate, Dibenzyl phosphoramidate, diphenyl phosphorua Midart, benzenesulfenamide, o-nitrobenzenesulfenamide (Nps), 2,4-dinitrobenzenesulfenamide, pentachlorobenzenesulfenamide, 2-nitro-4-methoxybenzenesulfenamide, triphenylmethylsulfen Amide, 3-nitropyridinesulfenamide (Npys), p-toluenesulfonamide (Ts), benzenesulfonamide, 2,3,6, -trimethyl-4-methoxybenzenesulfonamide (Mtr), 2,4,6 -Trimethoxybenzenesulfonamide (Mtb), 2,6-dimethyl-4-methoxybenzenesulfonamide (Pme), 2,3,5,6-tetramethyl-4-methoxybenzenesulfonamide (Mte), 4-methoxy Benzenesulfonamide (Mbs), 2,4,6-trimethylben Sulfonamide (Mts), 2,6-dimethoxy-4-methylbenzenesulfonamide (iMds), 2,2,5,7,8-pentamethylchroman-6-sulfonamide (Pmc), methanesulfonamide (Ms ), Β-trimethylsilylethanesulfonamide (SES), 9-anthracenesulfonamide, 4- (4 ′, 8′-dimethoxynaphthylmethyl) benzenesulfonamide (DNMBS), benzylsulfonamide, trifluoromethylsulfonamide, and phena And silsulfonamide.

  Exemplary protecting groups are detailed herein. However, it will be understood that the invention is not intended to be limited to these protecting groups. Rather, using the above classifications, a variety of additional equivalent protecting groups can be readily identified and utilized in the methods of the invention. In addition, a variety of protecting groups are described in Protective Groups in Organic Synthesis, 3rd edition, Greene, TW and Wuts, PG, John Wiley & Sons, New York (1999), the entire contents of which are herein Incorporated by reference.

  It will be understood that a compound may be substituted with any number of substituents or functional moieties as described herein. In general, the term “substituted” refers to whether or not the term is preceded by the term “optionally” and whether or not a substituent is included in the formulas of the invention. Refers to the replacement of a hydrogen radical in a given structure with a radical of a particular substituent. When more than one position in any given structure is substituted by more than one substituent selected from a particular group, the substituents may be the same or different at all positions Yes. As used herein, the term “substituted” is intended to include all permissible substituents of organic compounds. In a broad aspect, permissible substituents are acyclic and cyclic, branched and unbranched, carbocyclic and heterocyclic, aromatic and non-aromatic, organic. Contains substituents of compounds. A heteroatom such as nitrogen may have a hydrogen substituent and / or any permissible organic compound substituent that satisfies the valence of the heteroatom described herein. Furthermore, the present invention is not intended to be limited in any manner by the permissible substituents of organic compounds. The substituents and variable combinations represented by the present invention are preferably those that result in the formation of stable compounds useful, for example, in the treatment of infectious or proliferative disorders. The term “stable” as used herein preferably possesses sufficient stability to allow manufacturing, as well as a period sufficient to be detected, and preferably herein. Refers to a compound that maintains the integrity of the compound for a sufficient period of time useful for the purposes detailed in.

  The term “aliphatic”, as used herein, is both saturated and unsaturated, linear (ie, unbranched), branched, acyclic, cyclic, or polycyclic. Including fatty hydrocarbons of the formula, optionally substituted with one or more functional groups. As will be appreciated by those skilled in the art, “aliphatic” is intended herein to include, but is not limited to, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, and cycloalkynyl moieties. . Thus, as used herein, the term “alkyl” includes straight chain, branched chain and cyclic alkyl groups. Similar conventions apply to other general terms such as “alkenyl” and “alkynyl”. Further, as used herein, the terms “alkyl”, “alkenyl”, “alkynyl” and the like encompass both substituted and unsubstituted groups. In certain embodiments, as used herein, “lower alkyl” refers to those alkyl groups having 1 to 6 carbon atoms (cyclic, acyclic, substituted, unsubstituted, branched or non-cyclic). Used to show (branched).

In certain embodiments, the alkyl, alkenyl, and alkynyl groups employed in the invention contain 1-20 aliphatic carbon atoms. In certain other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the invention contain 1-10 aliphatic carbon atoms. In still other embodiments, the alkyl, alkenyl and alkynyl groups employed in the invention contain 1-8 aliphatic carbon atoms. In still other embodiments, the alkyl, alkenyl, and alkynyl groups used in the present invention contain 1-6 aliphatic carbon atoms. In still other embodiments, the alkyl, alkenyl, and alkynyl groups used in the invention contain 1-4 carbon atoms. Thus, exemplary aliphatic groups include, but are not limited to, for example, methyl, ethyl, n-propyl, isopropyl, cyclopropyl, —CH ₂ -cyclopropyl, vinyl, allyl, n-butyl, sec-butyl, isobutyl, tert- butyl, cyclobutyl, -CH ₂ - cyclobutyl, n- pentyl, sec- pentyl, isopentyl, tert- pentyl, cyclopentyl, -CH ₂ - cyclopentyl, n- hexyl, sec- hexyl, cyclohexyl, -CH ₂ - cyclohexyl moiety These may also include one or two or more substituents. Examples of alkenyl groups include, but are not limited to, ethenyl, propenyl, butenyl, 1-methyl-2-buten-1-yl, and the like. Representative alkynyl groups include, but are not limited to, ethynyl, 2-propynyl (propargyl), 1-propynyl, and the like.

Examples of some of the substituents of the above aliphatic (and other) moieties of the compounds of the present invention include, but are not limited to, aliphatic; heteroaliphatic; aryl; heteroaryl; arylalkyl; heteroarylalkyl; aryloxy; heteroalkoxy; heteroaryloxy; alkylthio; arylthio; heteroalkyl thio; _{heteroarylthio; -F; -Cl; -Br; -I} ; -OH; -NO 2; -CN; -CF 3; -CH 2 _{CF 3; -CHCl 2; -CH 2} OH; -CH 2 CH 2 OH; -CH 2 NH 2; -CH 2 SO 2 CH 3; -C (O) R x; -CO 2 (R x); - _{CON (R x) 2; -OC} (O) R x; -OCO 2 R x; -OCON (R x) 2; -N (R x) 2; -S (O) 2 R x; -NR _x (CO) R _x , wherein each occurrence of R _x independently includes, but is not limited to, aliphatic, heteroaliphatic, aryl, heteroaryl, arylalkyl or heteroarylalkyl; Here, any of the aliphatic, heteroaliphatic, arylalkyl or heteroarylalkyl substituents described above and herein are branched, whether substituted or unsubstituted. Can be unbranched, cyclic or acyclic, and where any of the aryl or heteroaryl substituents described above and herein are substituted May be substituted or unsubstituted. Further examples of commonly applicable substituents are illustrated by the specific embodiments described herein.

The term “heteroaliphatic” as used herein refers to an aliphatic moiety containing one or more oxygen, sulfur, nitrogen, phosphorus or silicon atoms, for example at the carbon atom position. Heteroaliphatic moieties may be branched, unbranched, cyclic or acyclic and include saturated and unsaturated heterocycles such as morpholino, pyrrolidinyl and the like. In certain embodiments, the heteroaliphatic moiety includes, but is not limited to, aliphatic; heteroaliphatic; aryl; heteroaryl; arylalkyl; heteroarylalkyl; alkoxy; aryloxy; heteroalkoxy; heteroaryloxy; alkylthio; arylthio; heteroalkyl thio; _{heteroarylthio; -F; -Cl; -Br; -I} ; -OH; -NO 2; -CN; -CF 3; -CH 2 CF 3; _{-CHCl 2; -CH 2 OH; -CH} 2 CH 2 OH; -CH 2 NH 2; -CH 2 SO 2 CH 3; -C (O) R x; -CO 2 (R x); - CON (R _{x) 2; -OC (O)} R x; -OCO 2 R x; -OCON (R x) 2; -N (R x) 2; -S (O) 2 R x; -N _{x (CO)} is replaced by the replacement independent according to one or more portions including R _x, wherein each occurrence of R _x is independently, but are not limited to, aliphatic, heteroaliphatic, aryl, Includes heteroaryl, arylalkyl or heteroarylalkyl, wherein any of the aliphatic, heteroaliphatic, arylalkyl or heteroarylalkyl substituents described above or herein are substituted or unsubstituted May be branched or unbranched, cyclic or acyclic, as described herein above or herein. Any of the aryl or heteroaryl substituents may be substituted or unsubstituted. Further examples of commonly applicable substituents are illustrated by the specific embodiments described herein.

  The terms “halo” and “halogen”, as described herein, refer to an atom selected from fluorine, chlorine, bromine and iodine.

The term “alkyl” includes linear alkyl groups (eg, methyl, ethyl, propyl, butyl, pentyl, hexyl, heptyl, octyl, nonyl, decyl, etc.), branched alkyl groups (isopropyl, tert-butyl, isobutyl, etc.) Etc.), cycloalkyl (alicyclic) groups (cyclopropyl, cyclopentyl, cyclohexyl, cycloheptyl, cyclooctyl), alkyl-substituted cycloalkyl groups, and saturated aliphatic groups including cycloalkyl-substituted alkyl groups. In some embodiments, the linear or branched alkyl is 6 or less (eg, C ₁ -C ₆ for straight chain, C ₃ -C ₆ for branched chain), more preferably 4 Or less carbon atoms in its skeleton. Likewise, preferred cycloalkyls have from 3-8 carbon atoms in their ring structure, and more preferably have 5 or 6 carbons in the ring structure. The term C ₁ -C ₆ includes alkyl groups containing ₁ to ₆ carbon atoms.

  Furthermore, unless otherwise specified, the term alkyl includes both “unsubstituted alkyl” and “substituted alkyl”, the latter of which independently replaces hydrogen on one or more carbons of the hydrocarbon backbone. Refers to an alkyl moiety having a substituent selected. Such substituents include, for example, alkenyl, alkynyl, halogen, hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, alkylcarbonyl, arylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl , Dialkylaminocarbonyl, alkylthiocarbonyl, alkoxyl, phosphate, phosphonate, phosphinate, cyano, amino (including alkylamino, dialkylamino, arylamino, diarylamino and alkylarylamino), acylamino (alkylcarbonylamino, arylcarbonylamino, carbamoyl) And ureido), amidino, imino, sul May include hydryl, alkylthio, arylthio, thiocarboxylate, sulfate, alkylsulfinyl, sulfonate, sulfamoyl, sulfonamide, nitro, trifluoromethyl, cyano, azide, heterocyclyl, alkylaryl, or aromatic or heteroaromatic moieties. . Cycloalkyls may be further substituted with, for example, the above substituents. An “alkylaryl” or “arylalkyl” moiety is an alkyl substituted with an aryl (eg, phenylmethyl (benzyl)). The term “alkyl” also includes the side chains of natural or unnatural amino acids. The term “n-alkyl” means a linear (ie, unbranched) unsubstituted alkyl group.

The term “alkenyl” includes unsaturated aliphatic groups similar to the alkyls described above with respect to length and possible substitution, but includes at least one double bond. For example, the term “alkenyl” includes straight chain alkenyl groups (eg, ethylenyl, propenyl, butenyl, pentenyl, hexenyl, heptenyl, octenyl, nonenyl, decenyl, etc.), branched alkenyl groups, cycloalkenyl (alicyclic) groups ( Cyclopropenyl, cyclopentenyl, cyclohexenyl, cycloheptenyl, cyclooctenyl), alkyl or alkenyl substituted cycloalkenyl groups, and cycloalkyl or cycloalkenyl substituted alkenyl groups. In certain embodiments, a straight chain or branched chain alkenyl group has 6 or fewer carbon atoms in its backbone (eg, C ₂ -C ₆ for straight chain, C ₃ for branched chain). ~C _6). Similarly, cycloalkenyl groups may have from 3 to 8 carbon atoms in their ring structure, and more preferably have 5 or 6 carbons in the ring structure. . The term C2-C6 includes alkenyl groups containing ₂ to ₆ carbon atoms.

  Further, unless otherwise specified, the term alkenyl includes both “unsubstituted alkenyl” and “substituted alkenyl”, the latter of which are independent, replacing hydrogen on one or more carbons of the hydrocarbon backbone. Refers to an alkenyl moiety having a substituent selected. Examples of the substituent include alkyl group, alkynyl group, halogen, hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, alkylcarbonyl, arylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkyl Aminocarbonyl, dialkylaminocarbonyl, alkylthiocarbonyl, alkoxyl, phosphate, phosphonate, phosphinate, cyano, amino (including alkylamino, dialkylamino, arylamino, diarylamino and alkylarylamino), acylamino (alkylcarbonylamino, arylcarbonylamino) Carbamoyl and ureido), amidino, imino, Mention may be made of hydryl, alkylthio, arylthio, thiocarboxylate, sulfate, alkylsulfinyl, sulfonate, sulfamoyl, sulfonamide, nitro, trifluoromethyl, cyano, azide, heterocyclyl, alkylaryl, or aromatic or heteroaromatic moieties. .

The term “alkynyl” includes unsaturated aliphatic groups similar to the alkyls described above with respect to length and possible substitution, but includes at least one triple bond. For example, the term “alkynyl” includes straight chain alkynyl groups (eg, ethynyl, propynyl, butynyl, pentynyl, hexynyl, heptynyl, octynyl, nonynyl, decynyl, etc.), branched alkynyl groups, and cycloalkyl or cycloalkenyl substituted alkynyl groups. including. In certain embodiments, a straight chain or branched chain alkynyl group has 6 or fewer carbon atoms in its backbone (eg, C ₂ -C ₆ for straight chain, C ₃ for branched chain). ~C _6). The term C2-C6 includes alkynyl groups containing ₂ to ₆ carbon atoms.

  Further, unless otherwise specified, the term alkynyl includes both “unsubstituted alkynyl” and “substituted alkynyl”, the latter of which are independent, replacing hydrogen on one or more carbons of the hydrocarbon backbone. Refers to an alkynyl moiety having a selected substituent. Examples of the substituent include alkyl group, alkynyl group, halogen, hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, alkylcarbonyl, arylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkyl Aminocarbonyl, dialkylaminocarbonyl, alkylthiocarbonyl, alkoxyl, phosphate, phosphonate, phosphinate, cyano, amino (including alkylamino, dialkylamino, arylamino, diarylamino and alkylarylamino), acylamino (alkylcarbonylamino, arylcarbonylamino) Carbamoyl and ureido), amidino, imino, Mention may be made of hydryl, alkylthio, arylthio, thiocarboxylate, sulfate, alkylsulfinyl, sulfonate, sulfamoyl, sulfonamide, nitro, trifluoromethyl, cyano, azide, heterocyclyl, alkylaryl, or aromatic or heteroaromatic moieties. .

  Unless stated otherwise specifically, “lower alkyl”, as described herein, is as described above, but represents an alkyl group having from 1 to 5 carbon atoms in its skeletal structure. means. “Lower alkenyl” and “lower alkynyl” have chain lengths of, for example, 2-5 carbon atoms.

  The term “alkoxy” includes substituted and unsubstituted alkyl, alkenyl, and alkynyl groups covalently bonded to an oxygen atom. Examples of alkoxy groups include methoxy, ethoxy, isopropyloxy, propoxy, butoxy, and pentoxy groups. A halogenated alkoxy group is mentioned as an example of a substituted alkoxy group. Alkoxy groups are alkenyl, alkynyl, halogen, hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, alkylcarbonyl, arylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl, dialkylamino Carbonyl, alkylthiocarbonyl, alkoxyl, phosphate, phosphonate, phosphinate, cyano, amino (including alkylamino, dialkylamino, arylamino, diarylamino and alkylarylamino), acylamino (alkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido) Amidino, imino, sulfhydryl, a) Independently selected, such as kirthio, arylthio, thiocarboxylate, sulfate, alkylsulfinyl, sulfonate, sulfamoyl, sulfonamido, nitro, trifluoromethyl, cyano, azide, heterocyclyl, alkylaryl, or aromatic or heteroaromatic moieties It may be substituted with a group. Examples of halogen substituted alkoxy groups include, but are not limited to, fluoromethoxy, difluoromethoxy, trifluoromethoxy, chloromethoxy, dichloromethoxy, trichloromethoxy and the like.

The term “heteroatom” includes atoms of any element other than carbon or hydrogen. Preferred heteroatoms are nitrogen, oxygen, sulfur and phosphorus.
The term “hydroxy” or “hydroxyl” includes groups with an —OH or —O ⁻ (with a suitable counterion).
The term “halogen” includes fluorine, bromine, chlorine, iodine and the like. The term “perhalogenated” generally refers to a moiety in which all hydrogens are replaced by halogen atoms.

The term “substituted” includes independently selected substituents, can be located on the moiety, and allows the molecule to perform its intended function. Examples of substituents include alkyl, alkenyl, alkynyl, aryl, (CR′R ″) _0-3 NR′R ″, (CR′R ″) _0-3 CN, NO ₂ , halogen, (CR ′ R ″) _0-3 C (halogen) ₃ , (CR′R ″) _0-3 CH (halogen) ₂ , (CR′R ″) _0-3 CH ₂ (halogen), (CR′R ′ ') _0-3 CONR'R ", (CR'R") _0-3 S (O) _1-2 NR'R ", (CR'R") _0-3 CHO, (CR'R '') _0-3 O (CR′R ″) _0-3 H, (CR′R ″) _0-3 S (O) _0-2 R ′, (CR′R ″) _0-3 O (CR′R ″) _0-3 H, (CR′R ″) _0-3 COR ′, (CR′R ″) _0-3 CO ₂ R ′ or (CR′R ″) _0-3 OR ′ groups; where each R ′ and R ″ are independently hydrogen, C ₁ -C ₅ alkyl, C _2- C ₅ alkenyl, C ₂ -C ₅ alkynyl or aryl group, or R ′ and R ″ together are a benzylidene group or a — (CH ₂ ) ₂ O (CH ₂ ) ₂ — group. .

  The term “amine” or “amino” includes compounds or moieties in which a nitrogen atom is covalently bonded to at least one carbon or heteroatom. The term “alkylamino” includes groups and compounds wherein the nitrogen is bound to at least one additional alkyl group. The term “dialkylamino” includes groups wherein the nitrogen atom is bound to at least two additional alkyl groups.

  The term “ether” includes compounds or moieties which contain an oxygen bonded to two different carbon atoms or heteroatoms. For example, the term includes “alkoxyalkyl”, which refers to an alkyl, alkenyl, or alkynyl group covalently bonded to an oxygen atom that is covalently bonded to another alkyl group.

  The terms “polynucleotide”, “nucleotide sequence”, “nucleic acid”, “nucleic acid molecule”, “nucleic acid sequence”, and “oligonucleotide” refer to a polymer of two or more nucleotides. The polynucleotide may be DNA, RNA or derivatives or modified versions thereof. The polynucleotide may be single-stranded or double-stranded. A polynucleotide may be modified at the base moiety, sugar moiety or phosphate backbone, for example, to improve the stability of the molecule, its hybridization parameters, and the like. The polynucleotide is 5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xanthine, 4-acetylcytosine, 5- (carboxyhydroxylmethyl) uracil, 5-carboxymethylaminomethyl-2 -Thiouridine, 5-carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylcuocin, inosine, N6-isopentenyladenine, 1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyl Adenine, 2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-adenine, 7-methylguanine, 5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil, beta-D-mannosi Queuosine, 5′-methoxycarboxymethyluracil, 5-methoxyuracil, 2-methylthio-N6-isopentenyladenine, wivetoxosin, pseudouracil, cuocin, 2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4- Thiouracil, 5-methyluracil, uracil-5-oxyacetic acid methyl ester, uracil-5-oxyacetic acid, 5-methyl-2-thiouracil, 3- (3-amino-3-N-2-carboxypropyl) uracil and 2 It may contain a modified base moiety selected from the group including but not limited to, 6-diaminopurine. A polynucleotide can be modified sugar moieties (eg, 2′-fluororibose, ribose, 2′-deoxyribose, 2′-O-methylcytidine, arabinose, and hexose) and / or modified phosphate moieties (eg, , Phosphorothioate and 5′-N-phosphoramidite linkages). Nucleotide sequences typically carry genetic information, including information used by cellular machinery to make proteins and enzymes. These terms include double-stranded or single-stranded genome and cDNA, RNA, any synthetic and genetically engineered polynucleotide, and both sense and antisense polynucleotides. It consists of single- and double-stranded molecules, ie DNA-DNA, DNA-RNA and RNA-RNA hybrids, and “protein nucleic acids” (PNA) formed by conjugating bases to the amino acid backbone. Including.

The term “base” refers to known purine and pyrimidine heterocyclic bases, deazapurines, and analogs thereof (including heterocyclic substituted analogs such as aminoethoxyphenoxazine), derivatives (eg 1-alkyl-, 1-alkenyl -, Heteroaromatic- and 1-alkynyl derivatives) and tautomers. Examples of purines include adenine, guanine, inosine, diaminopurine and xanthine, and analogs thereof (eg, 8-oxo-N ⁶ -methyladenine or 7-diazaxanthine) and derivatives. Pyrimidines include, for example, thymine, uracil and cytosine, and analogs thereof (eg, 5-methylcytosine, 5-methyluracil, 5- (1-propynyl) uracil, 5- (1-propynyl) cytosine and 4,4- Etanocytosine). Other examples of suitable bases include non-purinyl and non-pyrimidinyl bases such as 2-aminopyridine and triazines.

  In a preferred embodiment, the nucleomonomer of the oligonucleotide of the invention is an RNA nucleotide. In another preferred embodiment, the nucleonomer of the oligonucleotide of the invention is a modified RNA nucleotide. Thus, the oligonucleotide comprises a modified RNA nucleotide.

The term “nucleoside” includes a base covalently linked to a sugar moiety, preferably ribose or deoxyribose. Examples of preferred nucleosides include ribonucleosides and deoxyribonucleosides. A nucleoside also includes a base attached to an amino acid or amino acid analog, which may include a free carboxyl group, a free amino group, or a protecting group. Suitable protecting groups are well known in the art (see PGM Wuts and TW Greene, “Protective Groups in Organic Synthesis”, 2nd edition, Wiley-Interscience, New York (1999)).
The term “nucleotide” includes nucleosides that further include a phosphate group or phosphate analog.

  The nucleic acid molecule may be associated with a hydrophobic moiety for targeting and / or delivery of the molecule to the cell. In certain embodiments, the hydrophobic moiety is attached to the nucleic acid molecule via a linker. In certain embodiments, the binding is via a non-covalent interaction. In other embodiments, the binding is via a covalent bond. Any linker known in the art may be used to attach the nucleic acid to the hydrophobic moiety. Linkers known in the art include published international PCT applications WO 92/03464, WO 95/23162, WO 2008/021157, WO 2009/021157, WO 2009/134487, WO 2009/126933, US Patent Application Publication 2005 / 0107325, US Pat. No. 5,414,077, US Pat. No. 5,419,966, US Pat. No. 5,512,667, US Pat. No. 5,646,126 and US Pat. No. 5,652,359, which are incorporated herein by reference. The linker may be as simple as a covalent bond to a multi-atom linker. The linker may be cyclic or acyclic. The linker may be optionally substituted. In certain embodiments, the linker can be cleaved from the nucleic acid. In certain embodiments, the linker can be hydrolyzed under physiological conditions. In certain embodiments, the linker can be cleaved by an enzyme (eg, esterase or phosphodiesterase). In certain embodiments, the linker includes a spacer element for separating the nucleic acid from the hydrophobic moiety. The spacer element can contain 1 to 30 carbon or heteroatoms. In certain embodiments, the linker and / or spacer element comprises a protonatable functional group. Such protonatable functional groups can facilitate endosomal escape of nucleic acid molecules. Protonable functional groups can also aid in the delivery of nucleic acids to cells, for example by neutralizing the overall charge of the molecule. In other embodiments, the linker and / or spacer element is biologically inactive (ie, it does not impart biological activity or function to the resulting nucleic acid molecule).

In some embodiments, the nucleic acid molecule having a linker and a hydrophobic moiety is of the formula described herein. In some embodiments, the nucleic acid molecule has the formula:
In the formula,
X is N or CH;
A is a bond; substituted or unsubstituted, cyclic or acyclic, branched or unbranched aliphatic; or substituted or unsubstituted, cyclic or acyclic, branched A branched or unbranched heteroaliphatic;
R ¹ is a hydrophobic moiety;
R ² is hydrogen; oxygen protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted A branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched Chained aryl; substituted or unsubstituted, branched or unbranched heteroaryl; and R ³ is a nucleic acid.

In some embodiments, the molecule has the formula:
belongs to.

In some embodiments, the molecule has the formula:
belongs to.

In some embodiments, the molecule has the formula:
belongs to.

In some embodiments, the molecule has the formula:
belongs to.

In some embodiments, X is N. In some embodiments, X is CH.
In some embodiments, A is a bond. In some embodiments, A is a substituted or unsubstituted, cyclic or acyclic, branched or unbranched aliphatic. In some embodiments, A is acyclic, substituted or unsubstituted, branched or unbranched aliphatic. In some embodiments, A is an acyclic, substituted branched or unbranched aliphatic. In some embodiments, A is an acyclic, substituted unbranched aliphatic. In some embodiments, A is acyclic, substituted unbranched alkyl. In some embodiments, A is acyclic, substituted unbranched C _1-20 alkyl. In some embodiments, A is acyclic, substituted unbranched C _1-12 alkyl. In some embodiments, A is acyclic, substituted unbranched C _1-10 alkyl. In some embodiments, A is acyclic, substituted unbranched C _1-8 alkyl. In some embodiments, A is acyclic, substituted unbranched C _1-6 alkyl. In some embodiments, A is a substituted or unsubstituted, cyclic or acyclic, branched or unbranched heteroaliphatic. In certain embodiments, A is an acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic. In some embodiments, A is an acyclic, substituted branched or unbranched heteroaliphatic. In some embodiments, A is an acyclic, substituted unbranched heteroaliphatic.

In some embodiments, A is of the formula:
belongs to.

In some embodiments, A is of the formula:
belongs to.

In some embodiments, A is of the formula:
belongs to.

In some embodiments, A is of the formula:
belongs to.

In some embodiments, A is of the formula:
belongs to.

In some embodiments, A is of the formula:
belongs to.

In some embodiments, A is of the formula:
In the formula,
Each occurrence of R is independently a side chain of a natural or unnatural amino acid; and n is an integer from 1 to 20 (including 1 and 20). In some embodiments, A is of the formula:
belongs to.

  In certain embodiments, each occurrence of R is independently a side chain of a natural amino acid. In some embodiments, n is an integer from 1 to 15 (including 1 and 15). In some embodiments, n is an integer from 1 to 10 (including 1 and 10). In some embodiments, n is an integer from 1 to 5 (including 1 and 5).

In some embodiments, A is of the formula:
Of
In the formula, n is an integer of 1 to 20 (including 1 and 20). In some embodiments, A is of the formula:
belongs to.

  In some embodiments, n is an integer from 1 to 15 (including 1 and 15). In some embodiments, n is an integer from 1 to 10 (including 1 and 10). In some embodiments, n is an integer from 1 to 5 (including 1 and 5).

In some embodiments, A is of the formula:
Of
In the formula, n is an integer of 1 to 20 (including 1 and 20). In some embodiments, A is of the formula:
belongs to.

  In some embodiments, n is an integer from 1 to 15 (including 1 and 15). In some embodiments, n is an integer from 1 to 10 (including 1 and 10). In some embodiments, n is an integer from 1 to 5 (including 1 and 5).

In some embodiments, the molecule has the formula:
Of
Wherein X, R ¹ , R ² and R ³ are as defined herein; and A ′ is a substituted or unsubstituted, cyclic or acyclic, branched or Unbranched aliphatic; or substituted or unsubstituted, cyclic or acyclic, branched or unbranched heteroaliphatic.

In some embodiments, A ′ has the formula:
One of them.

In some embodiments, A is of the formula:
One of them.

In some embodiments, A is of the formula:
One of them.

In some embodiments, A is of the formula:
belongs to.

In some embodiments, A is of the formula:
belongs to.

In some embodiments, R ¹ is a steroid. In certain embodiments, R ¹ is cholesterol. In some embodiments, R ¹ is a lipophilic vitamin. In some embodiments, R ¹ is vitamin A. In some embodiments, R ¹ is vitamin E.

In some embodiments, R ¹ is of the formula:
Of
Wherein R ^A is substituted or unsubstituted, cyclic or acyclic, branched or unbranched aliphatic; or substituted or unsubstituted, cyclic or acyclic , Branched or unbranched heteroaliphatic.

In some embodiments, R ¹ is of the formula:
belongs to.

In some embodiments, R ¹ is of the formula:
belongs to.

In some embodiments, R ¹ is of the formula:
belongs to.

In some embodiments, R ¹ is of the formula:
belongs to.

In some embodiments, R ¹ is of the formula:
belongs to.

In some embodiments, the nucleic acid molecule has the formula:
In the formula,
X is N or CH;
A is a bond; substituted or unsubstituted, cyclic or acyclic, branched or unbranched aliphatic; or substituted or unsubstituted, cyclic or acyclic, branched A branched or unbranched heteroaliphatic;
R ¹ is a hydrophobic moiety;
R ² is hydrogen; oxygen protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted A branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched Chained aryl; substituted or unsubstituted, branched or unbranched heteroaryl; and R ³ is a nucleic acid.

In some embodiments, the nucleic acid molecule has the formula:
In the formula,
X is N or CH;
A is a bond; substituted or unsubstituted, cyclic or acyclic, branched or unbranched aliphatic; or substituted or unsubstituted, cyclic or acyclic, branched A branched or unbranched heteroaliphatic;
R ¹ is a hydrophobic moiety;
R ² is hydrogen; oxygen protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted A branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched Chained aryl; substituted or unsubstituted, branched or unbranched heteroaryl; and R ³ is a nucleic acid.

In some embodiments, the nucleic acid molecule has the formula:
In the formula,
X is N or CH;
A is a bond; substituted or unsubstituted, cyclic or acyclic, branched or unbranched aliphatic; or substituted or unsubstituted, cyclic or acyclic, branched A branched or unbranched heteroaliphatic;
R ¹ is a hydrophobic moiety;
R ² is hydrogen; oxygen protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted A branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched Chained aryl; substituted or unsubstituted, branched or unbranched heteroaryl; and R ³ is a nucleic acid.

In some embodiments, the nucleic acid molecule has the formula:
belongs to.

In some embodiments, the nucleic acid molecule has the formula:
belongs to.

In some embodiments, the nucleic acid molecule has the formula:
In which R ³ is a nucleic acid.

In some embodiments, the nucleic acid molecule has the formula:
Wherein R ³ is a nucleic acid; and n is an integer from 1 to 20 (including 1 and 20).

In some embodiments, the nucleic acid molecule has the formula:
belongs to.

In some embodiments, the nucleic acid molecule has the formula:
belongs to.

In some embodiments, the nucleic acid molecule has the formula:
belongs to.

In some embodiments, the nucleic acid molecule has the formula:
belongs to.

In some embodiments, the nucleic acid molecule has the formula:
belongs to.

As used herein, the term “linkage” includes an unmodified phosphodiester moiety (—O— (PO ^{2 —} ) — O—) that is covalently linked to a naturally occurring adjacent nucleomonomer. As used herein, the term “substitute linkage” includes any analog or derivative of a native phosphodiester group that is covalently linked to an adjacent nucleomonomer. Substitution bonds include phosphodiester analogs such as phosphorothioate, phosphorodithioate and P-ethyoxyphosphodiester, P-ethoxyphosphodiester, P-alkyloxyphosphodiester, methylphosphonate, and phosphorus Non-binding bonds such as acetals and amides. Such displacement bonds are known in the art (eg, Bjergarde et al. 1991. Nucleic Acids Res. 19: 5843; Caruthers et al. 1991. Nucleosides Nucleotides. 10:47). In some embodiments, non-hydrolyzable linkages such as phosphorothiate linkages are preferred.

In certain embodiments, the oligonucleotides of the invention comprise hydrophobically modified nucleotides or “hydrophobic modifications”. As used herein, a “hydrophobic modification” is one in which (1) the overall hydrophobicity of the base is significantly increased, and / or (2) the base is still similar to normal Watson-Crick interactions Refers to a base that has been modified so that can be formed. Examples of some non-limiting base modifications include phenyl, 4-pyridyl, 2-pyridyl, indolyl, and uridine and cytidine modifications at the 5-position such as isobutyl, phenyl (C ₆ H ₅ OH); tryptophanyl (C ₈ H ₆ N) CH ₂ CH (NH ₂ ) CO), isobutyl, butyl, aminobenzyl; phenyl; and naphthyl.

  Another type of conjugate that can bind to the end (3 'or 5' end), loop region or any other part of the sd-rxRNA is a sterol, sterol-type molecule, peptide, small molecule, protein, etc. Including. In some embodiments, the sdrxRNA may comprise more than one conjugate (of the same or different chemistry). In some embodiments, the conjugate is cholesterol.

  Another method for increasing target gene specificity or reducing off-target silencing is to use a 2 ′ modification (2′-O at the position corresponding to the second nucleotide at the 5 ′ end of the guide sequence. -Methyl modification etc.). This allows placement of this 2'-modification in the Dicer resistant hairpin structure, thereby designing better RNAi constructs with less or no off-target silencing It becomes possible to do.

  In one embodiment, the hairpin polynucleotide of the present invention can comprise one nucleic acid portion that is DNA and one nucleic acid portion that is RNA. The antisense (guide) sequence of the present invention may be a “chimeric oligonucleotide” comprising RNA-like and DNA-like regions.

  The term “RNase H activation region” includes a region of an oligonucleotide, eg, a chimeric oligonucleotide, that can recruit RNase H that cleaves a target RNA strand to which the oligonucleotide binds. Typically, the RNase activation region is a DNA or DNA-like nucleomonomer (at least about 3-5, typically about 3-12, more typically about 5-12, more preferably about 5-5. It contains 10 consecutive cores of nucleomonomers (see, eg, US Pat. No. 5,849,902). Preferably, the RNase H activation region comprises about 9 consecutive deoxyribose-containing nucleomonomers.

  The term “inactive region” includes antisense sequences, such as regions of chimeric oligonucleotides that do not mobilize or activate RNase H. Preferably, the non-activated region does not include phosphorothioate DNA. The oligonucleotide of the present invention comprises at least one non-activated region. In one embodiment, the non-activated region can be stable to a nuclease or can be complementary to a target and form a hydrogen bond with a target nucleic acid molecule that is bound by an oligonucleotide. Can provide specificity for the target.

In one embodiment, at least some of the contiguous polynucleotides are linked by substitution bonds, such as phosphorothioate bonds.
In some embodiments, most or all of the nucleotides beyond the guide sequence are linked by phosphorothioate linkages (whether 2 ′ modified or not). Such constructs tend to have improved pharmacokinetics due to their higher affinity for serum proteins. The phosphorothioate linkage in the non-guide sequence portion of the polynucleotide generally does not interfere with the activity of the guide strand once it has been loaded into the RISC.

  The antisense (guide) sequence of the present invention may comprise a “morpholino oligonucleotide”. Morpholino oligonucleotides are nonionic and function by an RNase H-independent mechanism. The four gene bases (adenine, cytosine, guanine, and thymine / uracil) of morpholino oligonucleotides are attached to a 6-membered morpholine ring. Morpholino oligonucleotides are made by joining four different subunit types, for example, by nonionic phosphorodiamidate intersubunit linkages. Morpholino oligonucleotides have a number of advantages including: complete resistance to nucleases (Antisence & Nucl. Acid Drug Dev. 1996. 6: 267); predictable targeting (Biochemica Biophysica Acta. 1999. 1489: 141) ); Certain activity in cells (Antisence & Nucl. Acid Drug Dev. 1997. 7:63); Excellent sequence specificity (Antisence & Nucl. Acid Drug Dev. 1997. 7: 151); Minimal non-antisense Activity (Biochemica Biophysica Acta. 1999. 1489: 141); and convenient osmotic or curettage delivery (Antisence & Nucl. Acid Drug Dev. 1997. 7: 291). Morpholino oligonucleotides are also preferred due to their non-toxicity at high doses. A discussion of the preparation of morpholino oligonucleotides can be found in Antisence & Nucl. Acid Drug Dev. 1997. 7: 187.

  The chemical modifications described herein are believed to facilitate loading of single-stranded polynucleotides into RISC based on the data described herein. Single-stranded polynucleotides have been shown to be active in loading into RISC and inducing gene silencing. However, the level of activity for a single-stranded polynucleotide is considered to be lower on a 2-4 digit scale when compared to a duplex polynucleotide.

  The present invention significantly increases (a) the stability of single-stranded polynucleotides, (b) facilitates efficient loading of polynucleotides into RISC complexes, and (c) cells by single-stranded nucleotides. Provides a description of chemical modification patterns that improve uptake. FIG. 18 provides some non-limiting examples of chemical modification patterns that may be beneficial for achieving the efficacy of single-stranded polynucleotides in cells. The chemical modification pattern can include a combination of ribose modification, backbone modification, hydrophobic nucleoside modification, and conjugate modification. Further, in some of the embodiments, the 5 'end of a single polynucleotide may be chemically phosphorylated.

  In yet another example, the present invention provides a description of chemical modification patterns that improve the function of RISC inhibitory polynucleotides. Single-stranded polynucleotides have been shown to inhibit the activity of preloaded RISC complexes through a substrate competition mechanism. For these types of molecules, commonly referred to as antagomers, activity usually requires high concentrations and in vivo delivery is not very effective. The present invention significantly increases (a) the stability of a single-stranded polynucleotide, (b) facilitates efficient recognition of the polynucleotide as a substrate by RISC, and / or (c) single-stranded by the cell. Provides a description of chemical modification patterns that improve nucleotide incorporation. FIG. 6 provides some non-limiting examples of chemical modification patterns that can be beneficial for achieving the efficacy of single-stranded polynucleotides in cells. The chemical modification pattern can include a combination of ribose modifications, backbone modifications, hydrophobic nucleoside modifications, and conjugate modifications.

  The modifications provided by the present invention are applicable to all polynucleotides. This includes single stranded RISC invasive polynucleotides, single stranded RISC inhibitory polynucleotides, conventional duplexed polynucleotides of various lengths (15-40 bp), asymmetric duplexed polynucleotides and the like. A polynucleotide may be modified by a variety of chemical modification patterns, including 5 'end modifications, ribose modifications, backbone modifications and hydrophobic nucleoside modifications.

Synthesis The oligonucleotide of the present invention can be synthesized by any method known in the art, for example, using enzymatic synthesis and / or chemical synthesis. Oligonucleotides can be synthesized in vitro (eg, using enzymatic and chemical synthesis) or in vivo (using recombinant DNA techniques well known in the art).

  In a preferred embodiment, chemical synthesis is used for the modified polynucleotide. Chemical synthesis of linear oligonucleotides is well known in the art and can be accomplished by solution or solid phase techniques. Preferably the synthesis is by a solid phase method. Oligonucleotides may be performed by any of a number of different synthetic procedures, including phosphoramidites, phosphite triesters, H-phosphonates and phosphotriester methods, typically by automated synthesis methods.

  Oligonucleotide synthesis protocols are well known in the art, eg, US Pat. No. 5,830,653; WO 98/13526; Stec et al. 1984. J. Am. Chem. Soc. 106: 6077; Stec et al. 1985 J. Org. Chem. 50: 3908; Stec et al. J. Chromatog. 1985. 326: 263; LaPlanche et al. 1986. Nucl. Acid. Res. 1986. 14: 9081; Fasman GD, 1989. 1989. CRC Press, Boca Raton, Fla .; Lamone. 1993. Biochem. Soc. Trans. 21: 1; US Patent No. 5,013,830; US Patent No. 5,214,135; US Patent No. 5,525,719; Kawasaki et al. 1993. J. Med. Chem. 36: 831; WO 92/03568; US Pat. No. 5,276,019; and US Pat. No. 5,264,423.

  The synthetic method chosen can depend on the length of the desired oligonucleotide, and such selection is within the skill of one of ordinary skill in the art. For example, the phosphoramidite and phosphite triester methods can produce oligonucleotides having 175 or more nucleotides, while the H-phosphonate method works well for oligonucleotides of less than 100 nucleotides. Function. When incorporating modified bases into oligonucleotides, and particularly when using modified phosphodiester linkages, the synthetic procedures are modified according to known procedures, if necessary. In this regard, Uhlmann et al. (1990, Chemical Reviews 90: 543-584) provide references and general procedures for making oligonucleotides with modified bases and modified phosphodiester linkages. Other exemplary methods for making oligonucleotides are taught in Sonveaux, 1994, “Protecting Groups in Oligonucleotide Synthesis”; Agrawal, Methods in Molecular Biology 26: 1. An exemplary synthesis method is also taught in "Oligonucleotide Synthesis-A Practical Approach" (Gait, M. J. IRL Press at Oxford University Press. 1984). Furthermore, linear oligonucleotides of defined sequence, including some sequences with modified nucleotides, are readily available from several commercial sources.

  Oligonucleotides can be purified by polyacrylamide gel electrophoresis or by a number of chromatographic methods including gel chromatography and high pressure liquid chromatography. To confirm the nucleotide sequence, particularly the unmodified nucleotide sequence, the oligonucleotide is Alternatively, it may be subjected to DNA sequencing by using selective chemical degradation of oligonucleotides bound to Hybond paper. Short oligonucleotide sequences can be analyzed by laser desorption mass spectrometry or by fast atom bombardment (McNeal, et al., 1982, J. Am. Chem. Soc. 104: 976; Viari, et al , 1987, Biomed. Environ. Mass Spectrom. 14:83; Grotjahn et al., 1982, Nuc. Acid Res. 10: 4671). Sequencing methods are also available for RNA oligonucleotides.

  The quality of the synthesized oligonucleotide is measured using capillary electrophoresis and degrading strong anion HPLC (SAX-) using, for example, the method of Bergot and Egan. 1992. J. Chrom. 599: 35. It can be evaluated by testing by HPLC).

  Other exemplary synthetic techniques are well known in the art (eg, Sambrook et al., Molecular Cloning: a Laboratory Manual, Second Edition (1989); DNA Cloning, Volumes I and II (DN Glover Ed. 1985); Oligonucleotide Synthesis (MJ Gait Ed, 1984; Nucleic Acid Hybridisation (BD Hames and SJ Higgins eds. 1984); A Practical Guide to Molecular Cloning (1984); or see the series Methods in Enzymology (Academic Press, Inc.)) .

  In certain embodiments, the RNAi construct of interest, or at least a portion thereof, is transcribed from an expression vector encoding the construct of interest. For this purpose, any art-recognized vector can be used. The transcribed RNAi construct can be isolated and purified prior to making the desired modifications (such as replacing the unmodified sense strand with a modified one).

Delivery / Carrier
Uptake of oligonucleotides by cells Oligonucleotides and oligonucleotide compositions are referred to as being contacted (ie, contacted or administered or delivered herein) with one or more cells or cell lysates. ). The term “cell” includes prokaryotic and eukaryotic cells, preferably vertebrate cells, and more preferably mammalian cells. In a preferred embodiment, the oligonucleotide composition of the present invention is contacted with a human cell.

  The oligonucleotide composition of the present invention can be used in vitro, eg, in a test tube or culture dish (which may or may not be introduced into a subject) or in vivo, eg, in a subject such as a mammalian subject. You may make it contact. In some embodiments, the oligonucleotide is administered locally or through electroporation. Oligonucleotides are taken up into cells at a slow rate by endocytosis, but endocytosed oligonucleotides are generally sequestered and cannot be utilized, for example, for hybridization to a target nucleic acid molecule. In one embodiment, cellular uptake can be facilitated by electroporation or calcium phosphate precipitation. However, these procedures are only useful in vitro or ex vivo and are not convenient and in some cases are associated with cytotoxicity.

  In another embodiment, delivery of the oligonucleotide to the cell is by any suitable art-recognized method including calcium phosphate, DMSO, glycerol or dextran, electroporation, or by transfection, e.g., cationic, anionic, Or using neutral lipid compositions or liposomes using methods known in the art (eg, WO 90/14074; WO 91/16024; WO 91/17424; US Pat. No. 4,897,355; Bergan et al. 1993). Nucleic Acid Research. 21: 3567). Enhanced oligonucleotide delivery can also be achieved with vectors (eg, Shi, Y. 2003. Trends Genet 2003 Jan. 19: 9; Reichhart JM et al. Genesis. 2002. 34 (1-2): 1604, Yu et al 2002. Proc. Natl. Acad Sci. USA 99: 6047; see Sui et al. 2002. Proc. Natl. Acad Sci. USA 99: 5515), virus, polyamine or polylysine, protamine or Ni, N12-bis ( Polycation conjugates using compounds such as ethyl) spermine (eg, Bartzatt, R. et al. 1989. Biotechnol. Appl. Biochem. 11: 133; Wagner E. et al. 1992. Proc. Natl. Acad. Sci. 88: 4255).

  In certain embodiments, the sd-rxRNA of the invention is described in US Provisional Application No. 61 / 310,611, filed March 4, 2010, entitled “Formulations and Methods for Targeted Delivery to Phagocyte Cells”, from which A variety of beta-glucan-containing particles, referred to as GeRPs (glucan encapsulated RNA loaded particles), incorporated by reference in the text, can be delivered. Such particles are also described in US Patent Publications US 2005/0281781 A1 and US 2010/0040656, and in PCT Publications WO 2006/007372 and WO 2007/050643, which are hereby incorporated by reference. The sd-rxRNA molecule may be hydrophobically modified and optionally associated with lipids and / or amphiphilic peptides. In certain embodiments, the beta-glucan particles are derived from yeast. In some embodiments, the payload capture molecule is a polymer, such as those having a molecular weight of at least about 1000 Da, 10,000 Da, 50,000 Da, 100 kDa, 500 kDa, and the like. Preferred polymers include (but are not limited to) cationic polymers, chitosan, or PEI (polyethyleneimine).

  Glucan particles can be derived from insoluble components of fungal cell walls, such as yeast cell walls. In some embodiments, the yeast is baker's yeast. Yeast-derived glucan molecules may include one or more of β- (1,3) -glucan, β- (1,6) -glucan, mannan and chitin. In some embodiments, the glucan particles comprise a hollow yeast cell wall so that the particles maintain a three-dimensional structure similar to cells in which the particles complex with molecules such as RNA molecules. Or it can be encapsulated. Some of the advantages associated with using yeast cell wall particles are the availability of the components, their biodegradable nature, and their ability to be targeted against phagocytic cells.

In some embodiments, the glucan particles are extracted by extraction of insoluble components from the cell wall, for example by extracting baker's yeast (Fleischmann's) with 1M NaOH / pH 4.0 H ₂ O, followed by washing and drying. Can be prepared. Methods for preparing yeast cell wall particles include U.S. Pat.Nos. 4,810,646, 4,992,540, 5,082,936, 5,028,703, 5,032,401, 5,322,841, 5,401,727, No. 5,607,677, No. 5,968,811, No. 6,242,594, No. 6,444,448, No. 6,476,003, US Patent Publication Nos. 2003/0216346, 2004/0014715 and No. 2010/0040656, and PCT Publication Applications Discussed in WO02 / 12348 and incorporated by reference from these.

  Protocols for preparing glucan particles are also described in and incorporated by reference from the following references: Soto and Ostroff (2008), “Characterization of multilayered nanoparticles encapsulated in yeast cell wall particles for DNA delivery.” Bioconjug Chem 19 (4): 840-8; Soto and Ostroff (2007), “Oral Macrophage Mediated Gene Delivery System”, Nanotech, Volume 2, Chapter 5 (“Drug Delivery”), pages 378-381; and Li et al. (2007), “Yeast glucan particles activate murine resident macrophages to secrete proinflammatory cytokines via MyD88-and Syk kinase-dependent pathways.”, Clinical Immunology 124 (2): 170-181.

  Glucan-containing particles such as yeast cell wall particles can also be obtained commercially. Some non-limiting examples include: Nutricell MOS 55 from Biorigin (Sao Paolo, Brazil), SAF-Mannan (SAF Agri, Minneapolis, Minn.), Nutrex (Sensient Technologies, Milwaukee, Wis.) , Alkali extracted particles such as those manufactured by Nutricepts (Nutricepts Inc., Burnsville, Minn.) And ASA Biotech, acid extracted WGP particles from Biopolymer Engineering, and Alpha-beta Technology, Inc. (Worcester, Mass.) Organic solvent extracted particles such as Adjuvax ™, and Novogen (Stamford, Conn.) Particulate glucan.

  Glucan particles such as yeast cell wall particles may have varying levels of purity depending on the method of manufacture and / or extraction. In some examples, the particles are alkali extracted, acid extracted or organic solvent extracted to remove intracellular components and / or outer mannoprotein layers of the cell wall. With such a protocol, particles having a glucan (w / w) content in the range of 50% to 90% can be produced. In some examples, lower purity, ie, particles with lower glucan w / w content are preferred, while in other embodiments, higher purity, ie particles with higher glucan w / w content, are preferred.

  Glucan particles such as yeast cell wall particles may have a natural lipid-containing material. For example, the particles are 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, Higher w / w lipids than 16%, 17%, 18%, 19%, 20% or 20% may be included. In the example section, the effectiveness of two glucan particle batches is tested: YGP SAF and YGP SAF + L (including natural lipids). In some instances, the presence of natural lipids can assist in complexing or capturing RNA molecules.

Glucan-containing particles typically have a diameter of about 2-4 microns, but particles having a diameter of less than 2 microns or greater than 4 microns are also compatible with aspects of the present invention.
The RNA molecule to be delivered is complexed with the glucan particles or “trapped” into its shell. As described in Soto and Ostroff (2008) Bioconjug Chem 19: 840 and now incorporated by reference, the particle shell or RNA component can be labeled for visualization. The method of loading GeRP is discussed further below.

  The optimal protocol for oligonucleotide uptake depends on a number of factors, the most important being the type of cell being used. Other factors that are important in uptake include, but are not limited to, the nature and concentration of the oligonucleotide, cell confluence, the type of culture in which the cells are contained (eg, suspension culture or plate culture) and the cells are grown. Examples include the type of medium.

Encapsulant Encapsulants encapsulate oligonucleotides in vesicles. In another aspect of the invention, the oligonucleotide may be associated with a carrier or vehicle, such as a liposome or micelle, although other carriers can be used as will be appreciated by those skilled in the art. Liposomes are vehicles made from lipid bilayers that have a structure similar to biological membranes. Such carriers are used to promote cellular uptake or targeting of the oligonucleotide or to improve the pharmacokinetic or toxicological properties of the oligonucleotide.

  For example, the oligonucleotide of the present invention is also contained in a liposome, which is a pharmaceutical composition containing an active ingredient dispersed or variously present in a body composed of an aqueous concentric layer adhered to a lipid layer. It may be administered in an encapsulated form. Oligonucleotides can be present both in the aqueous layer and in the lipid layer, or what is commonly referred to as a liposomic suspension, depending on the solubility. The hydrophobic layer is generally but not necessarily phospholipids such as lecithin and sphingomyelin, steroids such as cholesterol, de facto ionic surfactants such as diacetyl phosphate, stearylamine, or phosphatidylic acid, or hydrophobic Including other materials of sexual nature. Liposomes typically have a diameter in the range of about 15 nm to about 5 microns.

  The use of liposomes as a drug delivery vehicle offers several advantages. Liposomes increase intracellular stability, increase uptake efficiency, and improve biological activity. Liposomes are hollow spherical vesicles consisting of lipids arranged in a manner similar to the lipids that make up cell membranes. They have an internal aqueous space for encapsulating water-soluble compounds and are sized in the range of 0.05 to several microns in diameter. Several studies have shown that liposomes can deliver nucleic acids to cells and that nucleic acids remain biologically active. For example, lipid delivery vehicles originally designed as research tools, such as Lipofectin or LIPOFECTAMINE ™ 2000, can deliver intact nucleic acid molecules to cells.

  Specific advantages of using liposomes include: they are non-toxic and biodegradable in the composition; they exhibit a long circulation half-life; and recognition molecules are targeted to tissues For being able to easily bond to those surfaces. Finally, the production of cost-effective liposome-based pharmaceuticals, either in suspension or lyophilized products, has shown the feasibility of this technology as an acceptable drug delivery system.

  In some aspects, the formulations associated with the present invention may be selected for a class of saturated and unsaturated fatty acid residues that are naturally occurring, chemically synthesized, or modified. The fatty acids may be present in the form of triglycerides, diglycerides or individual fatty acids. In another embodiment, the use of well-verified fatty acid and / or lipid emulsion mixtures currently used in pharmacology for parenteral nutrition may be utilized.

  Liposome-based formulations are widely used for oligonucleotide delivery. However, most commercially available lipid or liposome formulations contain at least one positively charged lipid (cationic lipid). The presence of this positively charged lipid is believed to be essential to obtain a high degree of oligonucleotide loading and to enhance the membrane fusion properties of the liposomes. Several methods have been performed and published to identify the optimal positively charged lipid chemistry. However, commercially available liposomal formulations containing cationic lipids are characterized by a high level of toxicity. Due to limited in vivo therapeutic indices, liposome formulations containing positively charged lipids are toxic (ie, liver enzyme Has been shown to be accompanied.

  The nucleic acid related to the present invention may be hydrophobically modified and may be included in a neutral nanotransporter. Further description of neutral nanotransporters is incorporated by reference from PCT application PCT / US2009 / 005251, entitled “Neutral Nanotransporters.” Filed on September 22, 2009. Such particles allow quantitative incorporation of oligonucleotides into the uncharged lipid mixture. The lack of cationic lipid toxicity levels in such neutral nanotransporter compositions is an important feature.

  As shown in PCT / US2009 / 005251, oligonucleotides can be efficiently incorporated into lipid mixtures that do not contain cationic lipids, and such compositions allow therapeutic oligonucleotides to be incorporated into cells in a functional manner. Can be delivered efficiently. For example, high levels of activity were observed when the lipid mixture consisted of phosphatidylcholine-based fatty acids and sterols such as cholesterol. For example, one preferred formulation of a neutral lipid mixture consists of at least 20% DOPC or DSPC and at least 20% sterols such as cholesterol. A lipid to oligonucleotide ratio of only 1: 5 has been shown to be sufficient to obtain complete encapsulation of the oligonucleotide in an uncharged formulation.

  Neutral nanotransporter compositions allow for efficient loading of oligonucleotides into neutral lipid formulations. The composition may be modified in a manner that increases the hydrophobicity of the molecule (e.g., a hydrophobic molecule is bound to a hydrophobic molecule, either at the end of the oligonucleotide or at a non-terminal nucleotide, base, sugar or backbone (covalently or non- The oligonucleotides are (covalently) linked) and the modified oligonucleotides are mixed with a neutral lipid formulation (eg, containing at least 25% cholesterol and 25% DOPC or analogs thereof). Cargo molecules such as other lipids can also be included in the composition. This composition allows for efficient encapsulation of the oligonucleotide in neutral lipid particles when a portion of the formulation is built into the oligonucleotide itself.

  In some aspects, stable particles in the size range of 50-140 nm can be formed by complexing hydrophobic oligonucleotides with preferred formulations. The formulation by itself typically does not form small particles, but rather agglomerates, which can be converted to stable 50-120 nm particles by adding hydrophobically modified oligonucleotides. It is interesting to mention that it is converted.

  The neutral nanotransporter composition of the present invention comprises a hydrophobically modified polynucleotide, a neutral lipid mixture, and optionally a cargo molecule. A “hydrophobic modified polynucleotide” as used herein is a polynucleotide of the invention (ie, sd −) having at least one modification that renders the polynucleotide more hydrophobic than prior to modification of the polynucleotide. rxRNA). Modification can be accomplished by attaching (covalently or non-covalently) a hydrophobic molecule to the polynucleotide. In some examples, the hydrophobic molecule is a lipophilic group or comprises a lipophilic group.

  The term “lipophilic group” means a group that has a higher affinity for lipids than its affinity for water. Examples of lipophilic groups include, but are not limited to, cholesterol, cholesteryl or modified cholesteryl residues, adamantine, dihydrotesterone, long chain alkyl, long chain alkenyl, long chain alkynyl, oleyl-lithocholic acid, cholenoic acid, oleic acid Isoprenoids such as oil-cholenic acid, palmitic acid, heptadecylic acid, myristic acid, bile acid, cholic acid or taurocholic acid, deoxycholic acid, oleyl lithocholic acid, oleoylcholenoic acid, glycolipid, phospholipid, sphingolipid, steroid , Vitamins such as vitamin E, saturated or unsaturated fatty acids, fatty acid esters such as triglycerides, pyrenes, porphyrins, texaphyrin, adamantane, acridines, biotin, coumarin, fluorescein, loader Min, Texas-Red, digoxigenin, dimethoxytrityl, t-butyldimethylsilyl, t-butyldiphenylsilyl, cyanine dyes (eg, Cy3 or Cy5), Hoechst 33258 dyes, psoralen, or ibuprofen. The cholesterol moiety may be reduced (such as in cholestane) or substituted (eg by halogen). Combinations of different lipophilic groups in one molecule are also possible.

  Hydrophobic molecules can be attached at various positions on the polynucleotide. As noted above, the hydrophobic molecule may be attached to a terminal residue of the polynucleotide, such as 3 'to the 5' end of the polynucleotide. Alternatively, it may be linked to an internal nucleotide or a nucleotide on a branch of the polynucleotide. A hydrophobic molecule may be attached, for example at the 2 'position of the nucleotide. The hydrophobic molecule may also be bound to a heterocyclic base, sugar or backbone of the polynucleotide nucleotide.

  The hydrophobic molecule may be linked to the polynucleotide by a linker moiety. Optionally, the linker moiety is a non-nucleotide linker moiety. The non-nucleotide linker is, for example, an abasic residue (d spacer), an oligoethylene glycol such as triethylene glycol (spacer 9) or hexaethylene glycol (spacer 18), or an alkanediol such as butanediol. . The spacer units are preferably linked by phosphodiester or phosphorothioate linkages. The linker unit may appear only once in the molecule or may be incorporated several times, for example via a phosphodiester, phosphorothioate, methylphosphonate or amine linkage.

  An exemplary conjugation protocol involves the synthesis of a polynucleotide carrying an amino linker at one or more positions in the sequence, but no linker is required. The amino group is then reacted with the molecule to be conjugated using a suitable coupling or activating reagent. The conjugation reaction can be performed with the polynucleotide still bound to the solid support, or after cleavage of the polynucleotide in solution phase. Purification of modified polynucleotides by HPLC typically results in pure material.

  In some embodiments, the hydrophobic molecule is a sterol conjugate, phytosterol conjugate, cholesterol conjugate, sterol variant with altered side chain length that provides sufficient hydrophobicity to be incorporated into a micelle. Conjugates, fatty acid conjugates, any other hydrophobic group conjugates, and / or hydrophobic modifications of internal nucleosides.

For the purposes of the present invention, the term “sterol” or steroid alcohols refers to a subgroup of steroids having a hydroxyl group at the 3-position of the A ring. These are amphipathic lipids synthesized from acetyl-coenzyme A via the HMG-CoA reductase pathway. The overall molecule is extremely flat. The hydroxyl group on the A ring is polar. The rest of the aliphatic chain is nonpolar. Normally, sterols are considered to have an 8 carbon chain at the 17 position.
For the purposes of the present invention, the term “sterol-type molecule” refers to steroid alcohols, which are similar in structure to sterols. The main differences are the ring structure and the number of side chain carbons attached to position 21.
For the purposes of the present invention, the term “phytosterol” (also referred to as plant sterol) is a group of steroidal alcohols that are phytochemicals that occur naturally in plants. There are over 200 known phytosterols.

  For the purposes of the present invention, the term “sterol side chain” refers to the chemical composition of the side chain attached at position 17 of the sterol-type molecule. In a standard definition, sterols are limited to tetracyclic structures that carry an eight carbon chain at position 17. In the present invention, sterol-type molecules having longer and shorter side chains than conventional ones are described. The side chain may be a molecule or may contain a double skeleton.

  Thus, sterols useful in the present invention include, for example, cholesterol as well as unique sterols with side chains longer than 2-7 or 9 carbons attached at position 17. In certain embodiments, the length of the polycarbon tail varies between 5-9 carbons. Such conjugates may have significantly better in vivo efficacy, especially for delivery to the liver. These types of molecules are expected to function at concentrations that are 5 to 9 times lower than oligos conjugated to conventional cholesterol.

  Alternatively, the polynucleotide may be bound to a positively charged chemical that functions as a protein, peptide, or hydrophobic molecule. The protein can be selected from the group consisting of protamine, dsRNA binding domain, and arginine rich peptide. Exemplary positively charged chemicals include spermine, spermidine, cadaverine, and putrescine.

  In another embodiment, the hydrophobic molecule conjugate is combined with an optimal chemical modification pattern of a polynucleotide, including but not limited to hydrophobic modifications, phosphorothioate modifications, and 2 ′ ribo-modifications (herein). Higher potency may be demonstrated as described in detail).

  In another embodiment, the sterol-type molecule may be a naturally occurring phytosterol. The polycarbon chain may be longer than 9, linear, branched, and / or contain double bonds. Some phytosterols, including polynucleotide conjugates, can be significantly more potent and active in delivering polynucleotides to a variety of tissues. Some phytosterols may exhibit tissue preference and are therefore used as a means to deliver RNAi specifically to specific tissues.

  The hydrophobic modified polynucleotide is mixed with a neutral fatty acid mixture to form micelles. A neutral fatty acid mixture is a mixture of lipids with a net neutral or slightly net negative charge at or near physiological pH that can form micelles with hydrophobically modified polynucleotides. For the purposes of the present invention, the term “micelle” refers to small nanoparticles formed by a mixture of uncharged fatty acids and phospholipids. The neutral fatty acid mixture may contain cationic lipids as long as they are present in an amount that does not cause toxicity. In a preferred embodiment, the neutral fatty acid mixture does not contain a cationic lipid. A mixture free of cationic lipids is one in which less than 1%, preferably 0%, of the total lipids are cationic lipids. The term “cationic lipid” includes lipids and synthetic lipids that have a net positive charge at or near physiological pH. The term “anionic lipid” includes lipids and synthetic lipids that have a net negative charge at or near physiological pH.

Neutral lipids bind to the oligonucleotides of the invention by strong but non-covalent attraction (eg, electrostatic, van der Waals, pi-stacking, etc. interactions).
Neutral lipid mixtures include formulations selected from the class of naturally occurring, chemically synthesized or modified saturated and unsaturated fatty acid residues. The fatty acids can be present in the form of triglycerides, diglycerides or individual fatty acids. In another embodiment, well-known mixtures of fatty acids and / or lipid emulsions currently used for parenteral nutrition in pharmacology may be utilized.

  The neutral fatty acid mixture is preferably a mixture of fatty acids and sterols based on choline. Examples of fatty acids based on concentrated phosphorus include synthetic phosphocholine derivatives such as DDPC, DLPC, DMPC, DPPC, DSPC, DOPC, POPC, and DEPC. DOPC (Compound Registration No. 4235-95-4) is dioleoylphosphatidylcholine (dielideyl phosphatidylcholine, dioleoyl-PC, dioleoylphosphocholine, dioleoyl-sn-glycero-3-phosphocholine, dioleoylphosphatidylcholine known). DSPC (compound registration number 816-94-4 is distearoylphosphatidylcholine (also known as 1,2-distearoyl-sn-glycero-3-phosphocholine).

  The sterol in the neutral fatty acid mixture may be, for example, cholesterol. The neutral fatty acid mixture may consist entirely of choline-based fatty acids and sterols, or it may optionally contain cargo molecules. For example, the neutral fatty acid mixture may have at least 20% or 25% fatty acids and 20% or 25% sterols.

  For the purposes of the present invention, the term “fatty acid” relates to the conventional description of fatty acids. These can be present in individual entities or in the form of diglycerides and triglycerides. For the purposes of the present invention, the term “lipid emulsion” refers to a safe lipid formulation that is administered intravenously to a subject who cannot obtain sufficient lipid in the diet. This is an emulsion of soybean oil (or other naturally occurring oil) and egg phospholipids. Lipid emulsions are used for the formulation of some insoluble anesthetics. In the present disclosure, a lipid emulsion is a part of a commercial formulation such as Intralipid, Liposyn, Nutrilipid, a modified commercial formulation enriched with certain fatty acids, or a complete Or a combination of a fatty acid and a phospholipid prescribed in de novo.

  In one embodiment, cells that are contacted with the oligonucleotide composition of the invention are mixed with a mixture comprising the oligonucleotide and a lipid, eg, a mixture comprising one of the lipids or lipid compositions described above, for about 12 hours to about 24. Touch for hours. In another embodiment, the cells to be contacted with the oligonucleotide composition are contacted with a mixture comprising the oligonucleotide and a lipid, eg, a mixture comprising one of the lipids or lipid compositions described above, for about 1 to about 5 days. . In one embodiment, the cell is contacted with the mixture comprising lipid and oligonucleotide for about 3 days to about 30 days. In another embodiment, the lipid-containing mixture is placed in contact with the cells for at least about 5 to about 20 days. In another embodiment, the lipid-containing mixture is left in contact with the cells for at least about 7 to about 15 days.

  50% to 60% of the formulation may optionally be any other lipid or molecule. Such lipids or molecules are referred to herein as cargo lipids or cargo molecules. Cargo molecules include, without limitation, intralipids, small molecules, membrane fusion peptides or lipids, or other small molecules added to alter cellular uptake, release by endosomes, or tissue distribution characteristics May be. Where such properties are desired, the ability to resist cargo molecules is important for modifying the properties of these particles. For example, the presence of some tissue-specific metabolites can significantly change the tissue distribution profile. For example, the use of intralipid type formulations enriched in shorter or longer lipid chains with varying saturation levels will affect the tissue distribution profiles (and their loading) of these types of formulations .

  An example of a cargo lipid useful according to the present invention is a membrane fusion lipid. For example, the zwitterionic lipid DOPE (compound registration number 4004-5-1, 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine) is a preferred cargo lipid.

  Intralipid may consist of the following composition: 1000 mL contains: refined soybean oil 90 g, purified egg phospholipid 12 g, anhydrous glycerol 22 g, water for injection (sufficient to 1000 mL). The pH is adjusted to about pH 8 with sodium hydroxide. Energy content / L: 4.6 MJ (190 kcal). Osmotic pressure (about): 300 mOsm / kg of water. In another embodiment, the lipid emulsion comprises 5% safflower oil, 5% soybean oil, up to 1.2% egg phospholipid added as an emulsifier, and 2.5% glycerin in water for injection. Liposyn. This may also include sodium hydroxide for pH adjustment. pH 8.0 (6.0-9.0). Liposyn has an osmotic pressure of 276 mOsmol / liter (actual value).

  Variations in cargo lipid identity, amount and ratio affect the cellular uptake and tissue distribution characteristics of these compounds. For example, lipid tail length and saturation levels affect different uptake into liver, lung, fat and cardiomyocytes. The addition of special hydrophobic molecules such as vitamins or different forms of sterols can favor the distribution of specific compounds to specific tissues involved in metabolism. In some embodiments, vitamin A or E is used. Complexes are formed at different oligonucleotide concentrations, with higher concentrations favoring more efficient complex formation.

  In another embodiment, the lipid emulsion is based on a mixture of lipids. Such lipids include natural compounds, chemically synthesized compounds, purified fatty acids or any other lipid. In yet another embodiment, the composition of the lipid emulsion is completely artificial. In certain embodiments, the lipid emulsion is greater than 70% linoleic acid. In yet another specific embodiment, the lipid emulsion is at least 1% cardiolipin. Linoleic acid (LA) is an unsaturated omega-6 fatty acid. This is a colorless liquid consisting of a carboxylic acid having an 18-carbon chain and two cis double bonds.

  In yet another embodiment of the invention, alteration of the composition of the lipid emulsion is used as a means for changing the tissue distribution of the hydrophobically modified polynucleotide. This methodology results in specific delivery of polynucleotides to specific tissues

  In another embodiment, the lipid emulsion of the cargo molecule comprises greater than 70% linoleic acid (C18H32O2) and / or cardiolipin.

  Lipid emulsions such as intralipid have previously been used as delivery formulations for some water-insoluble drugs such as Propofol (re-formulated as Diprivan). A unique feature of the present invention is that (a) the modified polynucleotide is combined with a hydrophobic compound so that it can be incorporated into lipid micelles, and (b) to provide a reversible carrier. Mixing with a lipid emulsion. After injection into the bloodstream, micelles usually bind to albumin, HDL, LDL and other serum proteins. This binding is reversible and ultimately the lipid is absorbed by the cell. The polynucleotide that is taken up as part of the micelle is then delivered near the surface of the cell. Thereafter, cellular uptake can occur through a variety of mechanisms including, but not limited to, sterol-type delivery.

Complexing agents Complexing agents bind to the oligonucleotides of the invention through strong but non-covalent attractive forces (eg, electrostatic, van der Waals, pie stacking, etc. interactions). In one aspect, the oligonucleotides of the invention may be complexed with a complexing agent to increase cellular uptake of the oligonucleotide. An example of the complexing agent is a cationic lipid. Cationic lipids can be used to deliver oligonucleotides to cells. However, as noted above, formulations that do not contain cationic lipids are preferred in some embodiments.

  The term “cationic lipid” refers to lipids and synthetic lipids having both polar and non-polar domains that can be positively charged at or near physiological pH and bind to a polyanion such as a nucleic acid. Including those that facilitate delivery of cells into cells. In general, cationic lipids include saturated and unsaturated alkyl, and alicyclic ethers and esters of amines, amides, or derivatives thereof. Linear and branched alkyl and alkenyl groups of cationic lipids contain, for example, 1 to about 25 carbon atoms. Preferred straight chain or branched alkyl or alkene groups have 6 or more carbon atoms. Alicyclic groups include cholesterol and other steroid groups. Cationic lipids can be prepared with a variety of counter ions (anions) including, for example, Cl-, Br-, I-, F-, acetic acid, trifluoroacetic acid, sulfuric acid, nitrous acid and nitric acid.

  Examples of cationic lipids include polyethyleneimine, polyamidoamine (PAMAM) starburst dendrimer, lipofectin (combination of DOTMA and DOPE), lipofectase, LIPOFECTAMINE ™ (eg, LIPOFECTAMINE ™ 2000), DOPE, Cytofectin (Gilead Sciences, Foster City, Calif.), And Eufectins (JBL, San Luis Obispo, Calif.). Exemplary cationic liposomes are N- [1- (2,3-dioleoxy) -propyl] -N, N, N-trimethylammonium chloride (DOTMA), N- [1- (2,3-dioleoxy) sulfate. -Propyl] -N, N, N-trimethylammonium methyl (DOTAP), 3β- [N- (N ′, N′-dimethylaminoethane) carbamoyl] cholesterol (DC-Chol), 2,3, -dioleoyloxy -N- [2 (sperminecarboxamido) ethyl] -N, N-dimethyl-1-propanaminium trifluoroacetic acid (DOSPA), 1,2-dimyristyloxypropyl-3-dimethyl-hydroxyethylammonium bromide; and It can be produced from dimethyl dioctadecyl ammonium bromide (DDAB). Cationic lipids such as N- (1- (2,3-dioleyloxy) propyl) -N, N, N-trimethylammonium chloride (DOTMA) have been found to increase the antisense effect of phosphorothioate oligonucleotides by a factor of 1000. (Vlassov et al., 1994, Biochimica et Biophysica Acta 1197: 95-108). The oligonucleotide may be complexed with, for example, poly (L-lysine) or avidin, and the lipid may or may not be included in this mixture, for example, stearyl-poly (L-lysine). .

  Cationic lipids have been used in the art to deliver oligonucleotides to cells (eg, US Pat. Nos. 5,855,910; 5,851,548; 5,830,430; 5,780,053; 5,767,099; Lewis et al. 1996. Proc. Natl. Acad. Sci. USA 93: 3176; Hope et al. 1998. Molecular Membrane Biology 15: 1). Other lipid compositions that can be used to facilitate the uptake of the current oligonucleotide may be used in combination with the claimed methods. In addition to those listed above, other lipid compositions including those taught in, for example, U.S. Pat. No. 4,235,871; U.S. Pat. Nos. 4,501,728; 4,837,028; It is known.

  In one embodiment, the lipid composition further comprises an agent, eg, a viral protein (Kamata, et al., 1994. Nucl. Acids. Res. 22: 536) to enhance lipid-mediated transfection of oligonucleotides. But you can. In another embodiment, the oligonucleotide is contacted with the cell as part of a composition comprising an oligonucleotide, peptide and lipid, for example as taught in US Pat. No. 5,736,392. Improved lipids that are serum resistant have also been described (Lewis, et al., 1996. Proc. Natl. Acad. Sci. 93: 3176). Cationic lipids and other complexing agents act to increase the number of oligonucleotides that are carried into the cell through endocytosis.

  In another embodiment, N-substituted glycine oligonucleotides (peptoids) may be used to optimize oligonucleotide uptake. Peptoids have been used to make cationic lipid-like compounds for transfection (Murphy, et al., 1998. Proc. Natl. Acad. Sci. 95: 1517). Peptoids are prepared using standard methods (eg, Zuckermann, RN, et al. 1992. J. Am. Chem. Soc. 114: 10646; Zuckermann, RN, et al. 1992. Int. J. Peptide Protein Res. 40: 497). Liptoid, a combination of cationic lipids and peptoids, can also be used to optimize the uptake of the oligonucleotide of interest (Hunag, et al., 1998. Chemistry and Biology. 5: 345). . Liptoids can be synthesized by producing peptoid oligonucleotides and coupling amino-terminal submonomers to lipids through their amino groups (Hunag, et al., 1998. Chemistry and Biology. 5: 345).

  It is known in the art that positively charged amino acids can be used to make highly active cationic lipids (Lewis et al. 1996. Proc. Natl. Acad. Sci. US.A. 93: 3176). ). In one embodiment, a composition for delivering an oligonucleotide of the invention comprises a number of arginine, lysine, histidine or ornithine residues attached to a lipophilic moiety (see, eg, US Pat. No. 5,777,153).

  In another embodiment, a composition for delivering an oligonucleotide of the invention comprises a peptide having from about 1 to about 4 basic residues. These basic residues can be located, for example, at the amino terminus, C-terminus, or internal region of the peptide. Families of amino acid residues having similar side chains have been defined in the art. These families include basic side chains (eg, lysine, arginine, histidine), acidic side chains (eg, aspartic acid, glutamic acid), uncharged polar side chains (eg, glycine (which is also nonpolar) Asparagine, glutamine, serine, threonine, tyrosine, cysteine), non-polar side chains (eg alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta-branched side chains (eg Threonine, valine, isoleucine) and amino acids having aromatic side chains (eg tyrosine, phenylalanine, tryptophan, histidine). In addition to basic amino acids, the majority or all of the other residues of the peptide may be selected from non-basic amino acids such as amino acids other than lysine, arginine or histidine. Preferably, neutral amino acids having a long neutral side chain are dominant.

  In one aspect, a composition for delivering an oligonucleotide of the invention comprises a natural or synthetic polypeptide having one or more gamma carboxyglutamic acid residues, or γ-Gla residues. These gamma carboxyglutamic acid residues allow the polypeptides to bind to each other and to the membrane surface. In other words, a polypeptide having a series of γ-Gla can be used as a universal delivery modality to help an RNAi construct adhere to whatever membrane it contacts. This can at least delay the clearance of RNAi constructs from the bloodstream and enhance their chances of homing to the target.

  Gamma carboxyglutamic acid residues may be present in neutral proteins (eg, prothrombin is 10 γ-Gla residues). Alternatively, they may be introduced into purified, recombinantly purified, or chemically synthesized polypeptides by carboxylation, for example using a vitamin K-dependent carboxylase. The gamma carboxyglutamic acid residues may be continuous or non-contiguous, and the total number and position of such gamma carboxyglutamic acid residues in the polypeptide may vary depending on the “stickiness” of the polynucleotide at different levels. Can be adjusted / fine tuned to achieve.

  In one embodiment, the cells contacted with the oligonucleotide composition of the invention are mixed with a mixture comprising the oligonucleotide and a lipid, eg, a mixture comprising one of the lipids or lipid compositions described above, for about 12 hours to about 24 hours. Make contact. In another embodiment, the cells to be contacted with the oligonucleotide composition are contacted with a mixture comprising the oligonucleotide and a lipid, eg, a mixture comprising one of the lipids or lipid compositions described above, for about 1 day to about 5 days. In one embodiment, the cells are contacted with the mixture comprising lipid and oligonucleotide for a length of about 3 days to about 30 days. In another embodiment, the mixture comprising lipids is left in contact with the cells for at least about 5 to about 20 days. In another embodiment, the lipid-containing mixture is left in contact with the cells for at least about 7 to about 15 days.

  For example, in one embodiment, the oligonucleotide composition is as described herein in the presence of a lipid such as cytofectin CS or GSV (available from Glen Research; Sterling, Va.), GS3815, GS2888, etc. Alternatively, the cells may be contacted over an extended incubation period.

  In one embodiment, incubation with a mixture comprising cellular lipid and oligonucleotide composition does not reduce cellular viability. Preferably, after the transfection period, the cells are substantially alive. In one aspect, following transfection, the cells are at least about 70% to at least about 100% viable. In another embodiment, the cells are at least about 80% to at least about 95% viable. In yet another example, the cells are at least about 85% to at least about 90% viable.

  In one aspect, the oligonucleotide is modified by attaching a peptide sequence that transports the oligonucleotide referred to herein as a “transport peptide” into the cell. In one embodiment, the composition comprises an oligonucleotide that is complementary to a target nucleic acid molecule that encodes a protein and is covalently linked to a transport peptide.

  The term “transport peptide” includes an amino acid sequence that facilitates transport of an oligonucleotide into a cell. Exemplary peptides that facilitate transport of the portion to which it is bound into the cell are known in the art and include, for example, the HIV TAT transcription factor, lactoferrin, herpes VP22 protein, and fibroblast growth factor 2 ( Pooga et al. 1998. Nature Biotechnology. 16: 857; and Derossi et al. 1998. Trends in Cell Biology. 8:84; Elliott and O'Hare. 1997. Cell 88: 223).

  Oligonucleotides can be obtained using known techniques (eg, Prochiantz, A. 1996. Curr. Opin. Neurobiol. 6: 629; Derossi et al. 1998. Trends Cell Biol. 8:84; Troy et al. 1996. J. Neurosci. 16: 253, Vives et al. 1997. J. Biol. Chem. 272: 16010). For example, in one embodiment, an oligonucleotide carrying an activated thiol group is linked via its thiol group to a cysteine present in the transport peptide (eg, eg, Derossi et al. 1998. Trends Cell Biol. 8:84; Prochiantz. 1996. Current Opinion in Neurobiol. 6: 629; Allinquant et al. 1995. J Cell Biol. 128: 919 β turn between the second and third helices of the antennapedia homeodomain To the cysteine present therein). In another embodiment, the Boc-Cys- (Npys) OH group may be coupled to a transit peptide such that an oligonucleotide carrying the last (N-terminal) amino acid and SH group can be coupled to the peptide. (Troy et al. 1996. J. Neurosci. 16: 253).

In one embodiment, a linking group may be attached to the nucleomonomer and the transport peptide may be covalently attached to the linker. In one aspect, the linker can function both as a binding site for the transit peptide and as one that can provide stability against nucleases. Examples of suitable linkers, _C 1 _{-C 20} alkyl chain substituted or _{unsubstituted,} C 2 _{-C 20} alkenyl _chains, C 2 _{-C 20} alkynyl chains, peptides, and heteroatoms (e.g., S, O, NH, etc. ). Other exemplary linkers include bifunctional crosslinkers such as sulfosuccinidiyl-4- (maleimidophenyl) -butyric acid (SMPB) (see, eg, Smith et al. Biochem J 1991.276: 417-2). It is done.

  In one embodiment, the oligonucleotides of the invention are synthesized as molecular conjugates that utilize a receptor-mediated endocytosis mechanism for delivery of genes into cells (eg, Bunnell et al. 1992 Somatic Cell and Molecular Genetics. 18: 559 and references cited therein).

Delivery of targeting agent oligonucleotides can also be improved by targeting the oligonucleotides to cellular receptors. The targeting moiety can be conjugated to the oligonucleotide or can be conjugated to a carrier group (ie, poly (L-lysine) or liposome) attached to the oligonucleotide. This method is well suited for cells that exhibit specific receptor-mediated endocytosis.

  For example, oligonucleotide conjugates for 6-phosphomannosylated proteins are internalized 20 times more efficiently than free oligonucleotides by cells expressing mannose-6-phosphate specific receptors. Oligonucleotides may also be coupled to ligands for cellular receptors using biodegradable linkers. In another example, the delivery construct is mannosylated streptavidin that forms a strong complex with the biotinylated oligonucleotide. Mannosylated streptavidin was found to increase the internalization of biotinylated oligonucleotides 20-fold (Vlassov et al. 1994. Biochimica et Biophysica Acta 1197: 95-108).

  In addition, specific ligands may be conjugated to the polylysine component of the polylysine-based delivery system. For example, N-terminal membrane fusion peptide-polylysine conjugates of transferrin-polylysine, adenovirus-polylysine, and influenza virus hemagglutinin HA-2 significantly enhance receptor-mediated DNA delivery in eukaryotic cells. Mannosylated glycoproteins conjugated to poly (L-lysine) in alveolar macrophages have been used to enhance cellular uptake of oligonucleotides (Liang et al. 1999. Pharmazie 54: 559-566).

  Since malignant cells have a high need for essential nutrients such as folic acid and transferrin, these nutrients are used to target oligonucleotides to cancer cells. For example, when folic acid is conjugated to poly (L-lysine), enhanced oligonucleotide uptake is observed in promyelocytic leukemia (HL-60) cells and human melanoma (M-14) cells (Ginobbi et al. 1997. Anticancer Res. 17:29). In another example, liposomes coated with maleated bovine serum albumin, folic acid or protoporphyrin trivalent iron IX were used in mice macrophages, KB cells and 2.2.15 human hepatoma cells with enhanced oligonucleotides. Shows uptake by cells (Liang et al. 1999. Pharmazie 54: 559-566).

  Liposomes accumulate naturally in the liver, pancreas and retinal endothelial system (so-called passive targeting). By coupling liposomes to various ligands such as antibodies and protein A, they can be actively targeted to specific cell populations. For example, protein A-bearing liposomes may be pre-treated with an H-2K specific antibody targeted to an H-2K protein expressed on L cells encoded by the mouse major histocompatibility complex (Vlassov et al. 1994. Biochimica et Biophysica Acta 1197: 95-108).

  Other in vitro and / or in vivo RNAi reagent delivery is known in the art and can be used to deliver the RNAi construct of interest. For example, U.S. Patent Application Publication Nos. 20080152661, 20080112916, 20080107694, 20080038296, 20080070231392, 20060240093, 20060178327, 20060008910 and US Pat. No., 20050265957, No. 20050064595, No. 20050042227, No. 20050037496, No. 20050026286, No. 20040162235, No. 20040072785, No. 20040063654, No. 20030157030, WO 2008 / See 036825, WO04 / 065601 and AU2004206255B2 (all incorporated by reference).

The optimal route of administration or delivery of the administration oligonucleotide can vary depending on the desired outcome and / or subject being treated. As used herein, “administration” refers to contacting a cell with an oligonucleotide and can be performed in vitro or in vivo. To optimally reduce the expression of the protein translated from the target nucleic acid molecule, adjust the oligonucleotide dose without undue experimentation, for example as measured by RNA stability readout or by therapeutic response Can do.

  For example, the expression of the protein encoded by the nucleic acid target can be measured to determine if the dosing regimen needs to be adjusted accordingly. Furthermore, an increase or decrease in the level of RNA or protein in or produced by the cell may be measured using any art-recognized technique. By determining whether transcription has been reduced, the effectiveness of the oligonucleotide in inducing cleavage of the target RNA can be determined.

  Any of the above oligonucleotide compositions may be used alone or in combination with a pharmaceutically acceptable carrier. As used herein, “pharmaceutically acceptable carrier” includes suitable solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents and the like. Such media and agents for pharmaceutically active substances are well known in the art. Except where any conventional vehicle or agent is incompatible with the active ingredient, it can be used in a therapeutic composition. Supplementary active ingredients may also be incorporated into the compositions.

  Oligonucleotides may be incorporated into liposomes or polyethylene glycol modified liposomes or mixed with cationic lipids for parenteral administration. Incorporation of additional substances, such as antibodies reactive to membrane proteins found on specific target cells, into the liposomes helps target the oligonucleotide to specific cell types.

  For in vivo administration, the formulations of the present invention can be administered to a patient in a variety of forms adapted to deliver the construct to the eye. In a preferred embodiment, parenteral administration is to the eye. Administration to the eye can be intravitreal, intraanterior, subretinal, subconjunctival or subtenon.

  Pharmaceutical formulations for parenteral administration include aqueous solutions of the active compounds in water-soluble or water-dispersible form. In addition, suspensions of the active compounds as suitable oily injection suspensions may be administered. Suitable lipophilic solvents or vehicles include fatty oils such as sesame oil, or synthetic fatty acid esters such as ethyl oleate or triglycerides. Aqueous injection suspensions may contain substances which increase the viscosity of the suspension including, for example, sodium carboxymethyl cellulose, sorbitol or dextran, and optionally the suspension may also contain a stabilizer. The oligonucleotides of the invention may be formulated in a liquid solution, preferably a physiologically compatible buffer such as Hank's solution or Ringer's solution. Furthermore, the oligonucleotides may be formulated in solid form and redissolved or suspended just prior to use. Lyophilized forms are also included in the present invention.

  The selected method of delivery results in entry into the cell. In some embodiments, preferred delivery methods include liposomes (10-400 nm), hydrogels, controlled release polymers and other pharmaceutically applicable vehicles, and microinjection or electroporation (for ex vivo treatments). ).

  The pharmaceutical preparation of the present invention may be prepared and formulated as an emulsion. An emulsion is usually a homogeneous system in which one liquid is dispersed in another liquid, usually in the form of droplets having a diameter of more than 0.1 μm. The emulsion of the present invention may contain excipients such as emulsifiers, stabilizers, pigments, lipids, oils, fatty acids, fatty alcohols, fatty esters, wetting agents, hydrophilic colloids, preservatives, and antioxidants. If necessary, it may be present in the emulsion. The excipient can be present as a solution, as an aqueous phase, an oil phase, or as a separate phase itself.

  Examples of naturally occurring emulsifiers that can be used in the emulsion formulations of the present invention include lanolin, beeswax, phospholipids, lecithin and acacia. Finely divided solids have also been used as good emulsifiers in viscous formulations, especially in combination with surfactants. Finely divided solids that can be used as emulsifiers, non-swelling such as polar inorganic solids such as heavy metal hydroxides, bentonite, attapulgite, hectorite, kaolin, montmorillonite, colloidal aluminum silicate and colloidal aluminum magnesium silicate Clays, pigments, and nonpolar individuals such as carbon or glyceryl stearate.

  Examples of preservatives that can be used in emulsion formulations include methylparaben, propylparaben, quaternary ammonium salts, benzalkonium chloride, esters of p-hydroxybenzoic acid, and boric acid. Examples of antioxidants that can be used in emulsion formulations include free radical scavengers such as tocopherol, alkyl gallate, butylated hydroxyanisole, butylated hydroxytoluene, or reducing agents such as ascorbic acid and sodium disulfite, and citric acid Antioxidant synergist, such as tartaric acid and lecithin.

  In one embodiment, the oligonucleotide composition is formulated as a microemulsion. A microemulsion is a system of water, oil and amphiphile that is a single optically isotropic and thermodynamically stable solution. Typically, microemulsions contain sufficient amounts of a fourth component, typically moderate, to first disperse the oil in an aqueous surfactant solution and then form a clear system. By adding an alcohol of a chain length of

  Surfactants that can be used in the preparation of microemulsions include, but are not limited to, ionic surfactants, nonionic surfactants, Brij 96, polyoxyethylene oleyl ether, polyglycerol fatty acid esters, tetraglycerol monolaur. Rate (ML310), Tetraglycerol monooleate (MO310), Hexaglycerol monooleate (PO310), Hexaglycerol pentaoleate (PO500), Decaglycerol monocaprate (MCA750), Decaglycerol monooleate (MO750), Deca Glycerol sequiolate (S0750), decaglycerol decaoleate (DA0750) may be mentioned alone or in combination with a cosurfactant. Co-surfactants, usually short chain alcohols such as ethanol, 1-propanol and 1-butanol, penetrated into the surfactant film and were subsequently blocked by voids created between the surfactant molecules. Creating a film helps to increase interfacial fluidity.

  However, microemulsions can also be prepared without the use of co-surfactants, and self-emulsifying microemulsion systems that do not contain alcohol are known in the art. The aqueous phase may typically be, but is not limited to, water, aqueous drug solutions, glycerol, PEG300, PEG400, polyglycerol, propylene glycol and ethylene glycol derivatives. Oil phases include, but are not limited to, Captex 300, Captex 355, Capmul MCM, fatty acid esters, medium chain (C8-C12) mono, di and tri-glycerides, polyoxyethylated glyceryl fatty acid esters, fatty alcohols, poly Materials such as polyglycolized glycerides, saturated polyglycolized C8-C10 glycerides, vegetable oils and silicone oils.

  Microemulsions are particularly important in terms of drug solubilization and enhanced drug absorption. Lipid-based microemulsions (both oil / water and water / oil) have been proposed to enhance the oral bioavailability of drugs.

  Microemulsions improve drug solubilization, protect drugs from enzymatic hydrolysis, potential for enhanced drug absorption due to surfactant-induced changes in membrane fluidity and permeability, Provides ease, ease of oral administration to solid dosage forms, improved clinical efficacy, and reduced toxicity (Constantinides et al., Pharmaceutical Research, 1994, 11: 1385; Ho et al., J. Pharm. Sci., 1996, 85: 138-143). Microemulsions were also effective in transdermal delivery of active ingredients in both cosmetic and pharmaceutical applications. The microemulsion compositions and formulations of the present invention promote increased systemic absorption of oligonucleotides from the gastrointestinal tract, as well as local oligonucleotides in the gastrointestinal tract, vagina, oral cavity and other areas of administration. It is expected to improve uptake by cells.

  The useful dosage to be administered, and the particular mode of administration, are the cell type, for in vivo use, age, weight and particular animal and its area to be treated, the particular oligonucleotide used and delivery It will vary depending on the method, the intended therapeutic and diagnostic application, and the form of the formulation, such as a suspension, emulsion, micelle or liposome, which will be readily apparent to those skilled in the art. Typically, the dosage is administered at a lower amount and increased until the desired result is achieved. When using lipids to deliver oligonucleotides, the amount of lipid compound administered can vary and generally depends on the amount of oligonucleotide agent being administered. For example, the weight ratio of lipid compound to oligonucleotide agent is preferably about 1: 1 to about 15: 1, more preferably about 5: 1 to about 10: 1. In general, the amount of cationic lipid compound administered varies from about 0.1 milligrams (mg) to about 1 gram (g). For general guidance, typically about 0.1 mg to about 10 mg of a specific oligonucleotide agent and about 1 mg to about 100 mg of a lipid composition are administered for each kg of the patient's body weight. Higher and lower amounts may be used.

  The agents of the invention are administered to a subject or contacted with cells in a biologically compatible form suitable for pharmaceutical administration. “Biologically compatible form suitable for administration of a medicament” means that the oligonucleotide is administered in a form in which the therapeutic effect of the oligonucleotide exceeds any toxic effects. In one embodiment, the oligonucleotide is administered to the subject. Examples of controls include mammals such as humans and other primates; cattle, pigs, horses and farming (agricultural) animals; dogs, cats and other domestic pets; mice, rats and trans Examples include non-human transgenic animals.

  Administration of an active amount of an oligonucleotide of the invention is defined as an effective amount at the dosage and time required to achieve the desired result. For example, the amount of oligonucleotide activity is determined by the cell type, the oligonucleotide used, and the state of the disease for in vivo use, the age, sex and weight of the individual, and the oligonucleotide that elicits the desired response in the individual. It can change according to factors such as ability. Establishing therapeutic levels of oligonucleotides in cells depends on the rate of uptake and outward flow or degradation. Decreasing the extent of degradation extends the intracellular half-life of the oligonucleotide. Thus, chemically modified oligonucleotides, such as those with phosphate backbone modifications, may require different doses.

  The exact oligonucleotide dosage and number of doses administered will depend on the data generated experimentally and in clinical trials. Several factors affect the dosage, such as the desired effect, delivery vehicle, disease symptoms and route of administration. The dosage can be easily determined by those skilled in the art and can be formulated into the desired pharmaceutical composition. Preferably, the duration of treatment spans at least the entire course of disease symptoms.

  Dosage regimens can be adjusted to provide the optimum therapeutic response. For example, the oligonucleotide may be administered repeatedly, eg, several doses may be administered daily, or may be proportionally reduced as indicated by the requirements of the treatment situation. Whether the oligonucleotide is administered to a cell or to a subject, one of ordinary skill in the art can readily determine the appropriate dose and schedule of administration of the oligonucleotide of interest.

  Administration of sd-rxRNA to the eye, including intravitreal, intraanterior, subretinal, subconjunctival and subtenon administration, can be optimized through trials of dosing regimens. In some embodiments, a single administration is sufficient. As will be well known to those skilled in the art, sd-rxRNA may be administered in a sustained release formulation or device to further prolong the effect of the administered sd-rxRNA. The hydrophobic nature of sd-rxRNA compounds allows the use of a variety of polymers, some of which are not compatible with conventional oligonucleotide delivery.

  In other embodiments, the sd-rxRNA is administered multiple times. In some examples, it is daily, twice a week, once a week, once every two weeks, once every three weeks, once a month, once every two months, once every three months, every four months It is administered once, once every 5 months, once every 6 months, or less frequently than once every 6 months. In some examples, it is administered multiple times per day, week, month and / or year. For example, it is administered about every 2 hours, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 7 hours, 8 hours, 9 hours, 10 hours, every 12 hours, or every hour longer than 12 hours. be able to. It can be administered 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more than 10 times per day.

  Aspects of the invention relate to administering sd-rxRNA or rxRNA ori molecules to a subject. In some examples, the subject is a patient and administering the sd-rxRNA molecule comprises administering sd-rxRNA at the clinic.

  FIG. 1 demonstrates the uptake of sd-rxRNA 24 hours after intravitreal or subretinal administration. By 24 hours, sd-rxRNA penetrated all retinas. FIG. 2 shows a comparison of retinal uptake between sd-rxRNA and conventional RNAi compounds. Both are detected in the eye immediately after administration, whereas only sd-rxRNA is detected after 48 hours. FIG. 3 shows the detection of sd-rxRNA throughout the retina after intravitreal administration, but not the detection of conventional RNAi compounds. FIG. 4 shows that sd-rxRNA penetrates from the retina into the outer segment of the photoreceptor.

In some examples, the effective amount of sd-rxRNA delivered through ocular administration is at least about 0.05, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 8 , More than 90,91,92,93,94,95,96,97,98,99,100μg or 100 [mu] g (including any intermediate value).
Sd-rxRNA molecules administered through the methods described herein are efficiently targeted to all cell types in the eye.

  Physical methods for introducing nucleic acids include injection of solutions containing nucleic acids, bombardment with particles coated with nucleic acids, immersion of cells or organisms in solutions of nucleic acids, electroporation of cell membranes in the presence of nucleic acids Or topical administration to the eye of a composition comprising the nucleic acid. A viral construct packaged in a viral particle will achieve both efficient introduction of the expression construct into the cell and transcription of the nucleic acid encoded by the expression construct. Other methods known in the art for introducing nucleic acids into cells may be used, such as lipid-mediated carrier transport, chemically mediated transport such as calcium phosphate. Thus, nucleic acids can be introduced with components that perform one or more of the following activities: increasing nucleic acid uptake by cells, inhibiting single-stranded annealing, stabilizing single-stranded Or otherwise increasing the inhibition of the target gene.

Oligonucleotide Stability Assay In some embodiments, the oligonucleotides of the invention are stable, ie, substantially stable to endonuclease and exonuclease degradation. An oligonucleotide is considered to be substantially resistant to a nuclease if it is at least about 3 times more resistant to attack by endogenous cellular nucleases and is at least about more than the corresponding oligonucleotide. It is defined as highly nuclease resistant if it is 6 times more resistant. This can be demonstrated by showing that the oligonucleotides of the invention are substantially resistant to nucleases using techniques known in the art.

  One way in which substantial stability can be demonstrated is that the oligonucleotides of the invention function when delivered to a cell, for example, they reduce transcription or translation of a target nucleic acid molecule. By indicating, for example, by measuring protein levels or by measuring mRNA cleavage. Assays that measure the stability of the target RNA can be performed about 24 hours after transfection (eg, using Northern blot techniques, RNase protection assays, or QC-PCR, as is known in the art). . Alternatively, the level of the target protein may be measured. Preferably, in addition to testing the level of RNA or protein of interest, the level of RNA or protein of a control, non-target gene (eg, a subject having a sequence similar to the target) is preferred. Measure as a control. RNA or protein measurements can be performed using any art-recognized technique. Preferably, the measurement is started approximately 16-24 hours after transfection (MY Chiang, et al. 1991. J Biol Chem. 266: 18162-71; T. Fisher, et al. 1993. Nucleic Acid Research. 21 3857).

  The ability of the oligonucleotide compositions of the invention to inhibit protein synthesis can be measured by techniques known in the art, such as detecting inhibition of gene transcription or protein synthesis. For example, nuclease S1 mapping may be performed. In another example, Northern blot analysis may be performed to determine the presence of RNA encoding a particular protein. For example, total RNA may be prepared on a cesium chloride cushion (see, eg, Ausebel et al., 1987. Current Protocols in Molecular Biology (Greene & Wiley, New York)). The RNA is then used to perform a Northern blot and probe (see above, for example). In another example, the level of specific mRNA produced by the target protein can be measured using, for example, PCR. In yet another example, Western blots may be used to measure the amount of target protein present. In yet another embodiment, a phenotype affected by the amount of protein may be detected. Techniques for performing Western blots are well known in the art, see, eg, Chen et al. J. Biol. Chem. 271: 28259.

  In another example, the promoter sequence of the target gene may be bound to a reporter gene and transcription of the reporter gene may be monitored (eg, as described in detail below). Alternatively, an oligonucleotide composition that does not target the promoter may be identified by fusing a portion of the target nucleic acid molecule to the reporter gene such that the reporter gene is transcribed. By monitoring changes in expression of the reporter gene in the presence of the oligonucleotide composition, it is possible to determine the effectiveness of the oligonucleotide composition in inhibiting the expression of the reporter gene. For example, in one embodiment, an effective oligonucleotide composition reduces the expression of a reporter gene.

  A “reporter gene” is a nucleic acid that expresses a detectable gene product, which is RNA or protein. Detection of mRNA expression can be achieved by Northern blot, and protein detection can be achieved by staining with an antibody specific for the protein. A preferred reporter gene may be operably linked to a regulatory DNA sequence such that detection of the reporter gene product results in a measurement of the transcriptional activity of the regulatory sequence. In a preferred embodiment, the gene product of the reporter gene is detected by the intrinsic activity associated with that product. For example, a reporter gene may encode a gene product that produces a detectable signal based on color, fluorescence, or luminescence due to enzymatic activity. Examples of reporter genes include, but are not limited to, those that encode chloramphenicol acetyltransferase (CAT), luciferase, beta-galactosidase and alkaline phosphatase.

  One skilled in the art can readily recognize a number of reporter genes suitable for use in the present invention. These include, but are not limited to, chloramphenicol acetyltransferase (CAT), luciferase, human growth hormone (hGH) and beta-galactosidase. Examples of such reporter genes can be found in F. A. Ausubel et al., Current Protocols in Molecular Biology, John Wiley & Sons, New York (1989). Any gene that encodes a detectable product, eg, any product having detectable enzymatic activity or capable of generating a particular antibody, can be used as a reporter gene in the present methods.

  One reporter gene system is the firefly luciferase reporter system (Gould, S. J., and Subramani, S. 1988. Anal. Biochem., 7: 404-408 incorporated herein by reference). The luciferase assay is rapid and sensitive. In this assay, lysates of test cells are prepared and combined with ATP and the substrate luciferin. The encoded enzyme, luciferase, catalyzes the rapid ATP-dependent substrate oxidation to produce a luminescent product. The total light output is measured and proportional to the amount of luciferase present over a wide range of enzyme concentrations.

  CAT is another frequently used reporter gene system. The main advantage of this system is that it has been widely validated and is widely accepted as a measure of promoter activity (Gorman CM, Moffat, LF, and Howard, BH 1982. Mol. Cell Biol., 2: 1044-1051). In this system, test cells are transfected with a CAT expression vector and incubated with candidate substances within 2-3 days of the initial transfection. Thereafter, a cell extract is prepared. The extract is incubated with acetyl CoA and radioactive chloramphenicol. After incubation, the acetylated chloramphenicol is separated from the non-acetylated form by thin phase chromatography. In this assay, the degree of acetylation reflects the activity of the CAT gene by a particular promoter.

  Another suitable reporter gene system is based on immunological detection of hGH. This system is also fast and easy to use (Selden, R., Burke-Howie, K. Rowe, ME, Goodman, HM, and Moore, DD (1986), Mol. Cell, Biol., 6 : 3173-3179 incorporated herein by reference). The hGH system is advantageous in that the expressed hGH polypeptide is assayed in a solvent rather than a cell extract. This system therefore does not require destruction of the test cells. This reporter gene system is not limited to hGH, but rather is said to be suitable for use with any polypeptide for which an antibody with acceptable specificity is available or can be prepared. The principle should be understood.

  In one embodiment, the nuclease stability of a double-stranded oligonucleotide of the invention is measured and compared to a control, eg, an RNAi molecule typically used in the art (eg, a length of less than 25 nucleotides and a 2 nucleotide base overhang). Or a non-modified RNA duplex with blunt ends.

  The target RNA cleavage reaction achieved using the siRNA of the present invention is highly sequence specific. Sequence identity can be determined by sequence comparison and alignment algorithms known in the art. To determine the percent identity of two nucleic acid sequences (or two amino acid sequences), the sequences are aligned for optimal comparison purposes (eg, for optimal alignment, the first sequence or the second Introduce a gap in the sequence of A preferred non-limiting example of a local alignment algorithm utilized for sequence comparison is the algorithm of Karlin and Altschul (1990) Proc. Natl. Acad. Sci. USA 87: 2264-68, where Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90: 5873-77. Such an algorithm is incorporated into the BLAST program (version 2.0) of Altschul, et al. (1990) J. Mol. Biol. 215: 403-10. In addition, numerous companies such as Dharmacon and Invitrogen provide access to algorithms on their websites. The Whitehead Institute also offers a free siRNA selection program. More than 90% sequence identity between siRNA and target gene, eg up to 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence Identity is preferred. Alternatively, siRNA is functionally defined as a nucleotide sequence (or oligonucleotide sequence) that can hybridize to a portion of a target gene transcript. Examples of stringency conditions for polynucleotide hybridization are described in Sambrook, J., EF Fritsch and T. Maniatis, 1989, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 9th. Chapters and 11 and Current Protocols in Molecular Biology, 1995, edited by FM Ausubel et al., John Wiley & Sons, Inc., sections 2.10 and 6.3-6.4, which are incorporated herein by reference.

By inhibiting the expression of therapeutic use genes, the oligonucleotide compositions of the invention can be used to treat any disease that involves protein expression. As examples of diseases that can be treated with oligonucleotide compositions, for illustrative purposes only, cancer, retinopathy, autoimmune diseases, inflammatory diseases (ie, ICAM-1-related disorders, psoriasis, ulcerative colitis, clones) Disease), viral diseases (ie, HIV, hepatitis C), miRNA disorders, and cardiovascular diseases.
As discussed above, sd-rxRNA molecules administered by the methods described herein are efficiently targeted to all cell types in the eye.

  Aspects of the present invention include sd-rxRNA, ganglion cell layer (GCL), inner reticulated layer (IPL), inner granular layer (INL), outer reticulated layer (OPL), outer granular layer (ONL), rod cells And cone cell outer segment (OS), retinal pigment epithelium (RPE), rod and cone cell inner segment (IS), conjunctival epithelium, iris, ciliary body, corneum, and epithelium of eye sebaceous gland Targeting to a variety of cell types in the eye including, but not limited to, cells located in

  The sd-rxRNA targeted to the eye targets, in some instances, eye-specific genes or genes that are expressed at higher levels in the eye than in other tissues. As those skilled in the art will appreciate, publicly accessible databases may be used to identify genes that have eye-specific expression or increased expression in the eye relative to other tissues. Some non-limiting examples of such databases include the Tissue-Specific Genes Database (TISGED) and TiGER database for tissue-specific gene expression and regulation. In other embodiments, the sd-rxRNA does not target an eye specific gene. In other embodiments, the targeted gene does not have eye-specific expression or increased expression in the eye.

  In some examples, sd-rxRNA targeted to the eye is used to ameliorate at least one symptom of an eye-related condition or disorder. Some non-limiting examples of eye-related conditions or disorders include the following: Vascular leakage / angiogenesis (eg, angiographic cystic macular edema, retinal vein occlusion (RVO) Secondary macular edema, glaucoma or neovascular glaucoma (NVG), retinopathy of prematurity (ROP); fibroproliferative disorders (eg, proliferative vitreoretinopathy (PVR), epiretinal / vitreous macular adhesion; aging) Macular degeneration (AMD) (eg, exudative choroidal neovascularization (wet AMD), geographic atrophy (progressive atrophy AMD), early to mid-stage AMD); diabetic retinopathy (eg, nonproliferative diabetic retinopathy) (NPDR), diabetic macular edema (DME), proliferative diabetic retinopathy (PDR); retinal degenerative diseases (and related diseases); retinal vascular occlusion diseases (eg, retinal vein occlusion, retinal artery occlusion) and Other retinal diseases; retinal detachment; unknown cause (idiopathic Inflammatory diseases such as uveitis (including panuveitis) or choroiditis (including multifocal choroiditis) associated with diseases of the body or systemic (eg autoimmune); epidural or strong Birdshot retinochoroidopathy; Vascular diseases (retinal ischemia, retinal vasculitis, choroidal insufficiency, choroid thrombosis); optic nerve angiogenesis; optic neuritis; blepharitis; keratitis; iris angiogenesis Rubeosis iritis; Fuchs' heterochromic iridocyclitis; chronic uveitis or anterior uveitis; conjunctivitis; allergic conjunctivitis (seasonal or perennial, spring, atopic) Dry conjunctivitis (dry eye syndrome); iridocyclitis; iritis; scleritis; episclerosis; corneal edema; scleral disease; Uveitis; Po Naschlossman syndrome; Behcet's disease; Forked-Koyanagi-Harada syndrome; hypersensitivity reaction; conjunctival edema; venous congestion of the conjunctiva; periorbital cellulitis; acute lacrimal cystitis; nonspecific vasculitis; And / or dry conjunctivitis, a condition also known as dry eye, dry keratitis syndrome, xerophthalmia and dry eye syndrome (DES), which can result from increased tear film evaporation due to abnormal tear composition; Disorders associated with the immune diseases rheumatoid arthritis, lupus erythematosus, diabetes mellitus and Sjogren's syndrome In some embodiments, sd-rxRNA is administered as a method of wound healing. Non-limiting examples of eye related conditions or disorders are incorporated by reference from US Patent Publication No. 20100010082 and US Patent No. 6,331,313.

Angiogenesis / Vessel Leakage Aspects of the invention relate to treating diseases and conditions associated with angiogenesis and / or vascular leak. Of these conditions, wet AMD and DME are the most prevalent, macular edema secondary to PDR and RVO are less prevalent, and rare neovascular conditions include ROP and neovascular glaucoma. Vascular leakage is thought to be the driving force behind DME, while both vascular leakage and angiogenesis drive PDR. The oligonucleotide composition of the present invention can be selected based on the pathogenesis of a particular disease or condition. For example, compositions comprising anti-angiogenic oligonucleotides that affect vascular permeability can be selected to treat DME, while those that affect proliferation are selected to treat PDR. can do. Alternatively, the oligonucleotide composition comprises an anti-angiogenic agent, for example, an sd-rxRNA that inhibits the function of a target that affects vascular permeability and an sd-rxRNA that inhibits the function of a target that affects proliferation. , So that both etiological aspects of the condition are targeted.

  In certain embodiments, sd-rxRNA is used to treat angiogenesis and / or vascular permeability. In some embodiments, the sd-rxRNA targets vascular endothelial growth factor (VEGF), a vascular permeability inhibitor. VEGF is a classic and clinically validated target for the treatment of wet AMD and is expected to be approved for DME and RVO related MEs. VEGF protein is a growth factor that binds to tyrosine kinase receptors and is associated with multiple disorders such as cancer, age-related macular degeneration, rheumatoid arthritis, and diabetic retinopathy. Members of this protein family include VEGF-A, VEGF-B, VEGF-C and VEGF-D. Representative Genbank accession numbers providing DNA and protein sequence information for the human VEGF protein are NM_001171623.1 (VEGF-A), U43368 (VEGF-B), X94216 (VEGF-C) and D89630 (VEGF- D).

  Aspects of the invention relate to rxRNAori directed against VEGF. As described in the Examples section, over 100 optimal rxRNA ori sequences for VEGF were identified herein (Tables 2 and 9). rxRNAori can be directed against a sequence comprising at least 12 consecutive nucleotides of the sequences in Tables 2 or 9. For example, rxRNAori is directed against a sequence comprising 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or 25 consecutive nucleotides in Table 2 or 9 Can do. In some embodiments, rxRNAori is directed against a sequence comprising at least 12 contiguous nucleotides of SEQ ID NO: 13 (AUCACCAUCGACAGAACAGUCCUUA) or SEQ ID NO: 28 (CCAUGCAGAUUAUGCGGAUCAAACA). The sense strand of the rxRNAori molecule can comprise at least 12 contiguous nucleotides of a sequence selected from the sequences presented in Table 2. In some embodiments, the sense strand of rxRNAori comprises at least 12 contiguous nucleotides of the sequence of SEQ ID NO: 13 or SEQ ID NO: 28. The antisense strand of rxRNAori may be complementary to at least 12 consecutive nucleotides of a sequence selected from the sequences in Table 2. In some embodiments, the antisense strand of rxRNAori comprises at least 12 contiguous nucleotides of SEQ ID NO: 1377 (UAAGGACUGUUCUGUCGAUGGUGAU) or SEQ ID NO: 1378 (UGUUUGAUCCGCAUAAUCUGCAUGG).

  Non-limiting examples of rxRNAori directed against VEGF include rxRNAori comprising a sense strand comprising the sequence of SEQ ID NO: 13 and an antisense strand comprising the sequence of SEQ ID NO: 1377, or a sense comprising the sequence of SEQ ID NO: 28 And rxRNAori containing a strand and an antisense strand comprising the sequence of SEQ ID NO: 1378. It should be understood that a variety of modification patterns are compatible with rxRNAori. Aspects of the invention include rxRNAori directed against VEGF, wherein the rxRNAori is modified or unmodified. In some embodiments, rxRNAori is administered to the eye.

  Ori sequences may also be converted to sd-rxRNA molecules to target VEGF in the eye. It should be understood that the disclosed ori sequences represent non-limiting examples of sequences in VEGF for the development of sd-rxRNA. Variations in the length and modification of these sequences and other sequences in VEGF are also compatible with the development of sd-rxRNA molecules. The sd-rxRNA may be directed against a sequence selected from the sequences in Table 2 or 9. For example, the sd-rxRNA may be directed against a sequence comprising at least 12 consecutive nucleotides of a sequence selected from the sequences in Tables 2 or 9. In some embodiments, the sd-rxRNA is 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or a sequence selected from the sequences in Table 2 or 9 It may be directed against a sequence comprising 25 contiguous nucleotides.

  In some embodiments, the sd-rxRNA directed against VEGF comprises at least 12 nucleotides of a sequence selected from the sequences in Table 8. In some embodiments, the sense strand of sd-rxRNA comprises at least 12 contiguous nucleotides of the sequence of SEQ ID NO: 1317 (AGAACAGUCCUUA) or SEQ ID NO: 1357 (UGCGGAUCAAACA), and / or the antisense strand of sd-rxRNA , Comprising at least 12 contiguous nucleotides of the sequence of SEQ ID NO: 1318 (UAAGGACUGUUCUGUCGAU) or SEQ ID NO: 1358 (UGUUUGAUCCGCAUAAUCU). In certain embodiments, an sd-rxRNA directed against VEGF comprises a sense strand comprising SEQ ID NO: 1317 and an antisense strand comprising SEQ ID NO: 1318. A variety of chemical modification patterns are compatible with sd-rxRNA. Non-limiting examples of modified forms of SEQ ID NO: 1317 and SEQ ID NO: 1318 are SEQ ID NO: 1379 (AGAAmC. AGmU.mC.mC.mU.mU. A.Chl) and 1380 (P.mU, respectively). AAGGAfC.fU.G.fU.fU.fC.fU * G * fU * fC * G * A * U).

  In certain embodiments, an sd-rxRNA directed against VEGF comprises a sense strand comprising SEQ ID NO: 1357 and an antisense strand comprising SEQ ID NO: 1358. Non-limiting examples of modified forms of SEQ ID NO: 1357 and SEQ ID NO: 1358 are SEQ ID NO: 1397 (mU. G. mC. GGA mU. MC. AAAmC. A. Chl) and 1398 (P. mU, respectively). G.fU.fU.fU.GAfU.fC.fC.G.fC. A * fU * A * A * fU * fC * U). In certain embodiments, the sd-rxRNA comprises SEQ ID NOs: 1397 and 1398. It should be understood that other modification patterns of sd-rxRNA disclosed herein are also compatible with aspects of the present invention.

  Also described herein are sd-rxRNAs directed against genes that encode proteins other than VEGF. Non-limiting examples of such sd-rxRNA are provided in Tables 3-7. In some embodiments, the sd-rxRNA comprises at least 12 contiguous nucleotides of a sequence selected from the sequences in Tables 3-7.

  In some embodiments, the sd-rxRNA is directed against CTGF. Non-limiting examples of sd-rxRNAs directed against CTGF are provided in Table 5. In some embodiments, the sense strand of the sd-rxRNA directed against CTGF comprises at least 12 contiguous nucleotides of the sequence of SEQ ID NO: 1422 (GCACCUUUCUAGA), and the sd-rxRNA directed against CTGF The antisense strand comprises at least 12 contiguous nucleotides of the sequence of SEQ ID NO: 1423 (UCUAGAAAGGUGCAAACAU). Non-limiting examples of modified forms of SEQ ID NOs: 1422 and 1423 are SEQ ID NO: 947 (G.mC.A.mC.mC.mU.mU.mU.mC.mU. A * mG * mA. TEG-Chl) and 948 (P.mU.fC.fU.AGmA.A.mA.GGfU.G.mC * A * A * A * mC * A * U.). In some embodiments, the sense strand of sd-rxRNA directed against CTGF comprises at least 12 contiguous nucleotides of the sequence of SEQ ID NO: 1424 (UUGCACCUUUCUAA), and the sd-rxRNA directed against CTGF The antisense strand comprises at least 12 contiguous nucleotides of the sequence of SEQ ID NO: 1425 (UUAGAAAGGUGCAAACAAGG). Non-limiting examples of modified forms of SEQ ID NOs: 1424 and 1425 include SEQ ID NO: 963 (mU.mU.G.mC.A.mC.mC.mU.mU.mU.mC.mU * mA * mA.mA. TEG-Chl) and 964 (P.mU.fU.AGAmA.AGGfU.G.fC.mA.mA * mA * fC * mA * mA * mG * G.).

  In some embodiments, the sense strand of the sd-rxRNA directed against CTGF comprises at least 12 contiguous nucleotides of the sequence of SEQ ID NO: 947 or SEQ ID NO: 963. In certain embodiments, the sd-rxRNA directed against CTGF comprises a sense strand comprising the sequence of SEQ ID NO: 963 and an antisense strand comprising the sequence of SEQ ID NO: 964. In other embodiments, the sd-rxRNA directed against CTGF comprises a sense strand comprising the sequence of SEQ ID NO: 947 and an antisense strand comprising the sequence of SEQ ID NO: 948.

  The sd-rxRNA may be hydrophobically modified. For example, the sd-rxRNA may be bound to one or more hydrophobic conjugates. In some embodiments, the sd-rxRNA comprises at least one 5-methyl C or U modification.

  Aspects of the invention relate to compositions comprising the rxRNAori and / or sd-rxRNA nucleic acids described herein. The composition can include one or more rxRNAori and / or sd-rxRNA. In some embodiments, the composition comprises a plurality of different rxRNAoris directed against genes encoding different proteins and / or a plurality of different sd-rxRNAs directed against genes encoding different proteins. . In some embodiments, the composition comprises sd-rxRNA directed against VEGF and sd-rxRNA directed against another gene, such as a gene encoding CTGF or PTGS2 (COX-2) .

In some embodiments, one or more sd-rxRNAs target IGTA5, ANG2, CTGF, COX-2, complement factor 3 or 5, or combinations thereof.
In some embodiments, the sd-rxRNA targets connective tissue growth factor (CTGF), also known as hypertrophic chondrocyte specific protein 24. CTGF is a secreted heparin binding protein that has been linked to wound healing and scleroderma. Connective tissue growth factor is active in many cell types including fibroblasts, myofibroblasts, endothelial and epithelial cells. Exemplary Genbank accession numbers that provide DNA and protein sequence information for human CTGF are NM_001901.2 and M92934.

  In some embodiments, the sd-rxRNA comprises osteopontin (OPN), also known as secreted phosphoprotein 1 (SPP1), bone sialoprotein 1 (BSP-1) and early T lymphocyte activation (ETA-1). Target. SPP1 is a secreted glycoprotein type protein that binds to hydroxyapatite. OPN has been associated with a variety of biological processes including bone remodeling, immune function, chemotaxis, cell activation and apoptosis. Osteopontin is a fibroblast, proosteoblast, osteoblast, bone cell, odontoblast, bone marrow cell, hypertrophic chondrocyte, dendritic cell, macrophage, smooth muscle cell, skeletal myoblast, endothelial cell, and Produced by a variety of cell types, including extrabone (non-bone) cells in the inner ear, brain, kidney, decidua and placenta. Exemplary Genbank accession numbers that provide DNA and protein sequence information for human osteopontin are NM_000582.2 and X13694.

  In some embodiments, the sd-rxRNA targets the transforming growth factor β (TGFβ) protein, and there are three isoforms in mammals for transforming growth factor β (TGFβ1, TGFβ2, TGFβ3). ). TGFβ protein is a secreted protein belonging to a superfamily of growth factors involved in the regulation of many cellular processes including proliferation, migration, apoptosis, adhesion, differentiation, inflammation, immunosuppression and extracellular protein expression. These proteins are produced by a wide variety of cell types, including epithelial, endothelial, hematopoietic, neural and connective tissue cells. Representative Genbank accession numbers providing DNA and protein sequence information for human TGFβ1, TGFβ2 and TGFβ3 are BT007245, BC096235 and X14149, respectively. Within the TGFβ family, TGFβ1 and TGFβ2 are representative of suitable targets, but TGFβ3 is not. In some embodiments, the sd-rxRNA targets cyclooxygenase-2 (COX-2), also known as prostaglandin G / H synthase 2 (PTGS2). COX-2 is involved in lipid metabolism and biosynthesis of prostanoids and is associated with inflammatory disorders such as rheumatoid arthritis. A representative Genbank accession number providing DNA and protein sequence information for human COX-2 is AY462100.

  In other embodiments, the sd-rxRNA targets HIF-1α, a component of the HIF-1 transcription factor. HIF-1α is an important regulator of the regulation of cellular responses to hypoxia and acts upstream of the VEGF-dependent and VEGF-independent pro-angiogenic and fibrotic pathways. HIF-1α inhibitors are effective in laser CNV and OIR models. A representative Genbank accession number that provides DNA and protein sequence information for human HIF1α is U22431.

  In some embodiments, the sd-rxRNA targets mTOR. mTOR is a serine / threonine kinase component of the PI3K / Akt / mTOR pathway and a regulator of cell growth, proliferation, survival, transcription and translation. mTOR inhibitors have both anti-angiogenic (effective in laser CNV and OIR models) and anti-fibrotic activity. Rapamycin and other mTOR inhibitors are being used in clinical trials for AMD and DME. A representative Genbank accession number that provides DNA and protein sequence information for human mTOR is L34075.

  In some embodiments, the sd-rxRNA targets SDF-1 (stromal cell derived factor 1), a soluble factor that stimulates homing of hematopoietic stem cells and endothelial progenitor cells to tissue. SDF-1 acts synergistically with VEGF to drive pathogenic angiogenesis, and inhibition of SDF-1 signaling suppresses angiogenesis in OIR, laser CNV and VEGF-induced rodent models.

In certain embodiments, the sd-rxRNA targets PDGF-B (platelet derived growth factor B). Overexpression of PDGF-B in the retina in transgenic mice results in proliferation of vascular connective tissue, and inhibition of PDGF-B signaling enhances the efficacy of anti-VEGF treatment in the laser CNV model. Dual inhibition of PDGF-B and VEGF may promote NV regression. Exemplary Genbank accession numbers that provide DNA and protein sequence information for human PDGF genes and proteins include X03795 (PDGFA), X02811 (PDGFB), AF091434 (PDGFC), AB033832 (PDGFD).
In some embodiments, the sd-rxRNA targets TIE1 (tyrosine kinase with immunoglobulin-like and EGF-like domains).

  In other embodiments, the sd-rxRNA targets VEGFR1 (vascular endothelial growth factor receptor 1), also known as FLT1 (fms-related tyrosine kinase 1). This gene encodes a member of the vascular endothelial growth factor receptor (VEGFR) family. A VEGFR family member is the receptor tyrosine kinase (RTK), which is an extracellular ligand binding region with seven immunoglobulin (Ig) -like domains, a transmembrane segment, and a tyrosine kinase (TK) in the cytoplasmic domain. Includes domain. This protein binds to VEGFR-A, VEGFR-B and placental growth factor and plays an important role in angiogenesis and angiogenesis. Exemplary Genbank accession numbers that provide DNA and protein sequence information for human VEGFR1 genes and proteins include NM_001159920, NP_001153392, NM_001160030, NP_001153502, NM_001160031, NP_001153503, NM_002019 and NP_002010.

  In some embodiments, the sd-rxRNA targets VEGFR2 (vascular endothelial growth factor receptor 2), also known as KDR (kinase insert domain receptor). This receptor, known as the kinase insert domain receptor, is a type III receptor tyrosine kinase. It functions as a major mediator of VEGF-induced endothelial cell proliferation, survival, migration, tubular morphogenesis and budding. Signaling and intracellular transport of this receptor is regulated by multiple factors including Rab GTPase, P2Y purine nucleotide receptor, integrin alpha Vbeta3, T cell protein tyrosine phosphatase and the like. Exemplary Genbank accession numbers that provide DNA and protein sequence information for human VEGFR2 genes and proteins include NM_002253 and NP_002244. In some embodiments, the treatment of angiogenesis and / or vascular leakage may include the use of sd-rxRNA combinations where each sd-rxRNA targets a different gene. For example, sd-rRNA targeting VEGF and sd-rxRNA targeting HIF-1α may be used. As another example, sd-rRNA targeting mTOR and sd-rRNA targeting SDF-1 may be used. As yet another example, sd-rRNA targeting VEGF, sd-rRNA targeting mTOR, and sd-rRNA targeting PDGF-B may be used.

Wet AMD (choroidal neovascularization (CNV))
Aspects of the invention relate to treating choroidal neovascularization, which is the fastest form of progression of AMD (about 1 million cases in the United States) and new blood vessels from the choroid into the subretinal space Results from inadequate growth and leakage of fluid from these blood vessels. If untreated, 75% of patients progress to legal blindness within 3 years. Anti-VEGF agents in the vitreous can rapidly improve visual acuity by inhibiting the growth of CNV lesions and vascular leakage from CNV lesions. However, existing anti-VEGF agents cannot cause regression of existing lesions in most patients.

  In certain embodiments, sd-rxRNA is used to treat CNV. In some embodiments, the sd-rxRNA targets VEGF. In other embodiments, the sd-rxRNA targets HIF-1α, mTOR, PDGF-B, SDF-1, IGTA5, ANG2, CTGF, COX-2, or complement factor 3 or 5. In some embodiments, treatment of CNV includes the use of sd-rxRNA combinations where each sd-rxRNA targets a different gene.

Diabetic macular edema (DME)
DME results from vascular leakage from retinal blood vessels, resulting in fluid accumulation in the retinal macular that threatens vision and occurs in about 2-5% of diabetic patients. Current treatment standards are local or lattice laser photocoagulation. Intravitreal anti-VEGF agents and corticosteroids have been shown to be effective but have not yet been approved.

  In certain embodiments, sd-rxRNA is used to treat DMA. In some embodiments, the sd-rxRNA targets VEGF. In other embodiments, the sd-rxRNA targets HIF-1α, mTOR, PDGF-B, SDF-1, IGTA5, ANG2, CTGF, COX-2 or complement factor 3 or 5. In some embodiments, treatment of DME includes the use of sd-rxRNA combinations where each sd-rxRNA targets a different gene.

Proliferative diabetic retinopathy (PDR)
PDR is associated with chronic retinal ischemia. Retinal neovascularization occurs secondary to retinal ischemia and can lead to vitreous hemorrhage, vascular connective tissue proliferation, and tractional retinal detachment.
In certain embodiments, sd-rxRNA is used to treat PDR. In some embodiments, the sd-rxRNA targets VEGF. In other embodiments, the sd-rxRNA targets HIF-1α, mTOR, PDGF-B, SDF-1, IGTA5, ANG2, CTGF, COX-2 or complement factor 3 or 5. In some embodiments, treatment of PDR involves the use of sd-rxRNA combinations where each sd-rxRNA targets a different gene.

Macular edema secondary to RVO
RVO can occur in ischemic and non-ischemic forms. Ischemic RVO can lead to several vision-threatening complications including macular edema, retinal ischemia and angiogenesis. Non-ischemic RVO has a more favorable prognosis, and the most common vision threatening complication is macular edema.
In certain embodiments, the sd-rxRNA is used to treat macular edema secondary to RVO. In some embodiments, the sd-rxRNA targets VEGF. In other embodiments, the sd-rxRNA targets HIF-1α, mTOR, PDGF-B, SDF-1, IGTA5, ANG2, CTGF, COX-2 or complement factor 3 or 5. In some embodiments, treatment of macular edema secondary to RVO includes the use of sd-rxRNA combinations in which each sd-rxRNA targets a different gene.

Iris Angiogenesis / Neovascular Glaucoma (NVG)
NVG is a rare disorder that develops in eyes suffering from severe chronic eye ischemia. The most common cause is progressive PDR or ischemic CRVO. Iris neovascularization occurs due to ischemia and eventually occludes the trabecular meshwork leading to severe secondary glaucoma.
In some embodiments, sd-rxRNA is used to treat iris angiogenesis and / or NVG. In some embodiments, the sd-rxRNA targets VEGF. In other embodiments, the sd-rxRNA targets HIF-1α, mTOR, PDGF-B, SDF-1, IGTA5, ANG2, CTGF, COX-2 or complement factor 3 or 5. In some embodiments, treatment of iris angiogenesis and / or NVG includes the use of sd-rxRNA combinations in which each sd-rxRNA targets a different gene.

Proliferative retinal disease Proliferative retinal disease, proliferative vitreoretinopathy, proliferative diabetic retinopathy (PDR), epiretinal membrane (transparent layer of cells that can grow on the surface of the retinal macular, retina ) And wet AMD.
In certain embodiments, sd-rxRNA is used to treat proliferative retinal disease. In some embodiments, sd-rxRNA targets TGFβ, while in other embodiments, sd-rxRNA targets CTGF. In yet other embodiments, multiple sd-rxRNAs target PDGFRα, mTOR, IGTA5, or combinations thereof. In yet other embodiments, the plurality of sd-rxRNAs target TGFβ and at least one of CTGF, PDGFRα, mTOR, IGTA5, or combinations thereof. In further embodiments, the plurality of sd-rxRNAs target CTGF and at least one of TGFβ, PDGFRα, mTOR, IGTA5, or combinations thereof. In certain embodiments, the treatment of proliferative retinal disease comprises the use of sd-rxRNA combinations in which each sd-rxRNA targets a different gene.

Dry AMD
In some embodiments, the sd-rxRNA comprises map-like atrophy (GA) (a form of dry AMD that progresses slower than wet AMD) and early to mid-stage atrophy AMD (atrophic preceding GA or CNV) Used to treat atrophic AMD, including the early stages of AMD. In some embodiments, the sd-rxRNA targets Alu transcription. In other embodiments, the sd-rxRNA is DICER (an endoribonuclease in the RNase III family, wherein double-stranded RNA (dsRNA) and pre-microRNA (miRNA) are referred to as small interfering RNA (siRNA). Target transcription factors or other molecules that inhibit or regulate the expression of short double stranded RNA fragments 20-20 nucleotides long).

Cystic macular edema Cystic macular edema is the accumulation of intraretinal fluid in erofoveal cysts after surgery. In certain embodiments, sd-rxRNA is used to treat cystoid macular edema. In some embodiments, the sd-rxRNA targets the COX-2 (cyclooxygenase-2) enzyme.

Retinitis pigmentosa Retinitis pigmentosa is an inherited retinal degenerative disease caused by mutations in several known genes. In certain embodiments, sd-rxRNA is used to treat retinitis pigmentosa. In some embodiments, the sd-rxRNA targets NADPH oxidase.

Glaucoma Glaucoma is a slowly progressive disease characterized by optic nerve degeneration. There is an initial loss of vision in the periphery and a loss of central vision in the stage of disease progression. The most understood risk factor for glaucoma-related vision loss is intraocular pressure (IOP). Trabeculectomy is a surgical procedure designed to create a channel or bleb through the sclera to drain excess fluid from the anterior portion of the eye, resulting in decreased IOP . The most common cause of trabeculectomy failure is bleb blockage by scar tissue.

  In certain embodiments, sd-rxRNA is used to prevent scar formation resulting from trabeculectomy. In some embodiments, sd-rxRNA targets CTGF, while in other embodiments, sd-rxRNA targets TGFβ. In still other embodiments, multiple sd-rxRNAs target both CTGF and TGFβ. In some embodiments, scar tissue formation is prevented by use of a combination of sd-rxRNAs, one targeting CTGF and the other targeting TGFβ.

Uveitis Uveitis is a broad group of disorders characterized by inflammation of the middle layer of the eye consisting of the choroid, ciliary body and iris, called the uveitis. This disorder is anatomically classified as anterior, intermediate, posterior or panuveitis and pathologically classified as infectious or non-infectious.

  In certain embodiments, sd-rxRNA is used to treat uveitis. In some embodiments, the sd-rxRNA targets a cytokine, eg, TNFα. In other embodiments, the sd-rxRNA targets IL-1, IL-6, IL-15, IL-17, IL-2R, or CTLA-4. In yet other embodiments, the sd-rxRNA targets an adhesion molecule comprising VLA-4, VCAM-1, LFA-1, ICAM-1, CD44 or osteopontin. In yet another embodiment, the sd-rxRNA is TNFα, IL-1, IL-6, IL-15, IL-17, IL-2R, CTLA-4, VLA-4, VCAM-1, LFA-1, ICAM -1, targeting at least one of CD44 and osteopontin. In some embodiments, scar tissue formation is prevented by the use of sd-rxRNA combinations, each targeting a different gene.

Retinoblastoma (Rb)
Retinoblastoma is a cancer that develops rapidly in cells of the retina. In certain embodiments, sd-rxRNA is used to treat retinoblastoma. In some embodiments, the sd-rxRNA targets HMGA2, a nuclear protein thought to have a role in neoplastic transformation.

  In certain embodiments, the sd-rxRNAs of the invention can be used for multigene silencing. In some embodiments, sd-rxRNA combinations are used to target multiple different genes. For example, when used for the treatment of neovascular disorders, sd-rxRNA targeting VEGF can be used with sd-rxRNA targeting HIF-1α. As another example, when used to treat uveitis, a combination of sd-rxRNA targeting TNFα, sd-rxRNA targeting VCAM-1 and sd-rxRNA targeting IL-2R May be used.

  In some embodiments, VEGF, IGTA5, ANG2, CTGF, COX-2, complement factor 3, complement factor 5, HIF-1α, mTOR, SDF-1, PDGF-β, Alu, NADPH oxidase, TGF-β , IL-1, IL-6, IL-15, IL-17, IL-2R, CTLA-4, VLA-4, VCAM-1, LFA-1, ICAM-1, CD44, osteopontin (SPP1), or these Multiple sd-rxRNAs can be used to target any combination of In some embodiments, such multi-target gene silencing can be used to treat more than one disease or condition, if necessary.

In some embodiments, the sd-rxRNA targets MAP4K4. MAP4K4 is a mammalian serine / threonine protein kinase and belongs to the group of protein kinases related to Saccharomyces cerevisiae Sterile 20 (STE20). MAP4K4 (aka, NIK as Nck interactor computing kinase (N ck i nteracting k inase) ) was first identified in mice screening for proteins that interact with the SH3 domain of Nck (Su et al. (1997 )) . Since its discovery, MAP4K4 has been associated with a wide range of physiological functions.

  An approach for RNAi-mediated inhibition of MAP4K4 expression is described in US Provisional Application No. 61 / 199,661, filed November 19, 2008, titled “Inhibition of MAP4K4 through RNAi”, and November 19, 2009. It is described in the filed PCT application PCT / US2009 / 006211, titled “Inhibition of MAP4K4 through RNAi”, incorporated herein by reference. An sd-rxRNA molecule that targets MAP4K4 can be adapted to aspects of the invention. In some embodiments, an sd-rxRNA molecule targeting VEGF and an sd-rxRNA molecule targeting MAP4K4 may be administered together.

Table 1 presents non-limiting examples of sd-rxRNA targets and the areas where they can be applied.

  In one embodiment, treatment of cells in vitro with an oligonucleotide is for ex vivo treatment of cells removed from a subject or for treatment of cells that are not derived from a subject but are to be administered to a subject ( For example, it can be used for removal of the expression of transplanted antigen in cells to be transplanted into a subject). In addition, it is designed to treat cells in vitro, in non-therapeutic settings, for example to assess gene function, to study gene regulation and protein synthesis, or to regulate gene expression or protein synthesis. Can be used to evaluate the improvements made to the oligonucleotide. Treatment of cells in vivo can be useful in certain clinical settings where it is desirable to inhibit protein expression. The target nucleic acid is human, non-human primate, non-human mammal, non-human vertebrate, rodent (mouse, rat, hamster, rabbit, etc.), domestic animal, pet (cat, dog etc.), Xenopus, fish Used in RNAi-based therapy in any animal having an RNAi pathway, such as insects (such as Drosophila), and C. elegans.

  The present invention provides a method for inhibiting or preventing a disease or condition associated with abnormal or undesirable target gene expression or activity in a subject by administering to the subject a nucleic acid of the present invention. . Where appropriate, subjects are first treated with a priming agent to be more responsive to subsequent RNAi therapy. A subject at risk for a disease caused by or contributed to by an abnormal or undesirable target gene expression or activity is identified, for example, by any or any combination of diagnostic or prognostic assays known in the art can do. Administration of the prophylactic agent may be performed prior to the manifestation of symptoms characteristic of the abnormality of the target gene, or may be performed with a delay in the progression thereof, so that the disease or disorder is prevented. Depending on the type of abnormality of the target gene, for example, a target gene, target gene agonist or target gene antagonist can be used to treat the subject.

  In another aspect, the invention relates to a method for modulating target gene expression, protein expression or activity for therapeutic purposes. Thus, in an exemplary embodiment, the methods of the invention allow cells capable of expressing a target gene to be specific for the target gene or protein (eg, specific for the mRNA encoded by said gene). Or specifying the amino acid sequence of the protein) and contacting the nucleic acid of the invention such that one or more of the expression or activity of the target protein is modulated. These methods can be performed in vitro (eg, by culturing cells with the agent), in vivo (eg, by administering the agent to a subject), or ex vivo. Typically, a subject may be treated with a priming agent, if desired, first to be more responsive to subsequent RNAi therapy. Accordingly, the present invention provides a method of treating an individual suffering from a disease or disorder characterized by abnormal or undesirable expression or activity of a target gene polypeptide or nucleic acid molecule. Inhibition of target gene activity is desirable in situations where the target gene is not abnormally controlled and / or reduced target gene activity may have beneficial effects.

  Accordingly, the therapeutic agents of the invention can be administered to a subject to treat (prophylactically or therapeutically) disorders associated with abnormal or undesirable target gene activity. In combination with such treatment, pharmacogenomics (ie, study of the relationship between an individual's genotype and the individual's response to a foreign compound or drug) may be considered. Differences in the metabolism of a therapeutic agent can result in severe toxicity or treatment failure by changing the relationship between pharmacologically active drug dose and blood concentration. Thus, physicians or clinicians can gain in relevant pharmacogenomic studies in deciding whether or not to administer a therapeutic agent and in adjusting the dosage and / or therapeutic regimen of treatment with a therapeutic agent. You may consider applying knowledge. Pharmacogenomics corresponds to clinically important genetic variations in response to drugs due to changes in drug disposition and abnormal effects in affected individuals.

  For purposes of the present invention, ranges may be expressed herein as from “about” one particular value and / or from “about” one other particular value. is there. When such a range is expressed, another aspect includes from the one particular value and / or to the other particular value. Similarly, when values are expressed as approximations, by use of the aforementioned “about,” it will be understood that the particular value forms another aspect. Further, it is understood that each endpoint of the range is important in relation to other endpoints and independent of the other endpoints.

  Further, for purposes of the present invention, the term “a” or “an” entity refers to one or more of that entity. For example, “a protein” or “a nucleic acid molecule” refers to one or more of these compounds, or at least one compound. Thus, the terms “a” (or “an”), “one or more”, and “at least one” can be used interchangeably herein. The terms “comprising”, “including”, and “having” can also be used interchangeably. Further, a compound “selected from the group consisting of” refers to one or more of the compounds in the list that follows, and includes a mixture (ie, combination) of two or more of the compounds. According to the present invention, an isolated or biologically pure protein or nucleic acid molecule is a compound that has been removed from its natural environment. Thus, “isolated” or “biologically pure” does not necessarily reflect the extent to which the compound has been produced. Isolated compounds of the present invention may be obtained from their natural sources, produced using molecular biological techniques, or produced by chemical synthesis.

  The invention is further illustrated by the following examples, which should in no way be construed as further limiting. The entire contents of all references cited throughout this application, including academic literature, issued patents, published patent applications and co-pending patent applications, are hereby expressly incorporated by reference. .

Example
Example 1 Ocular Administration of sd-rxRNA Molecules Subretinal and intravitreal administration was found to be highly effective in delivering sd-rxRNA molecules to all intraocular cell types. MAP4K4 targeted or non-targeted sd-rxRNA (with or without DY547 label) was injected either by subretinal or intravitreal administration. A dose of 5 and 10 μg was evaluated. No signs of inflammation were observed. The eye appeared healthy and no signs of cell migration (an indicator of inflammatory response) were observed.

  Compound uptake was visualized by fundus microscopy. Mice were euthanized at 24 and 48 hours, retinas were harvested, fixed, paraffin embedded and compound uptake and distribution analyzed by confocal microscopy.

  FIG. 1 shows DIC, DY547 and Hoechst confocal triple images. As revealed by staining, by 24 hours, sd-rxRNA penetrated the entire retina. FIG. 2 provides a comparison of delivery between sd-rxRNA and traditional RNAi compounds. 10 μg RNA in 1 μl PBS was delivered intravitreally. Fundus imaging with white light confirmed that the retina had normal eye structure and no gross signs of bleeding or inflammation. Fluorescence imaging was performed with a fundus camera (a camera with a weak magnification microscope designed to image the internal surface of the eye). As revealed in FIG. 2, both sd-rxRNA and traditional RNAi compounds were detected in the retina immediately after administration. However, only sd-rxRNA molecules were detected after 24 and 48 hours.

FIG. 3 reveals that sd-rxRNA was detected in the entire retina after intravitreal administration of sd-rxRNA, but not after administration of PBS or traditional RNAi compounds.
FIG. 4 demonstrates that sd-rxRNA penetrates the retina into the outer segment of the photoreceptor.
FIG. 5 demonstrates that in ARPE-19 cells, sd-rxRNA exhibits strong uptake and silencing compared to rxRNAori.
FIG. 6 shows some non-limiting examples of sd-rxRNA for use in ocular indications.

The efficacy of sd-rxRNA directed against VEGF is shown in FIG. 7, which shows the percentage of VEGF mRNA levels (normalized to PPIB) after administration of VEGF-specific sd-rxRNA. ).
FIG. 8 demonstrates the efficient penetration of sd-rxRNA after intravitreal administration.
Fluorescently labeled RNAi compound was administered to the mouse eye using 1 μl of intravitreal injection. By 2-3 hours after injection, sd-rxRNA was present in the ganglion cell layer and in the photoreceptor outer segment by 24 hours after administration. Fluorescence was detected using a laser scanning confocal microscope.

  FIG. 9 demonstrates that sd-rxRNA is significantly taken up in the retina, but not rxRNAori, at 24 hours in vivo. A fluorescence-tagged RNAi compound was administered, and an all-ocular mount was prepared from the eyes collected 24 hours after the administration. All eyes were fixed overnight with 4% paraformaldehyde, then fixed with formalin and embedded in paraffin. Cross sections were cut (thickness 5 μm), stained with Hoechst, and visualized using a Leica SP5 confocal microscope. The image shown is a triple overlay of Hoechst, DY547 (red tag on RNAi compound) and differential interference contract (DIC) image. Panel B shows a higher magnification observation from the sd-rxRNA sample shown in panel A (scale bar is 10 μm), which reveals delivery to retinal pigment epithelial cells.

  Figures 10 and 11 reveal significant uptake of sd-rxRNA 24 hours after administration in the rabbit retina. Fluorescently labeled RNAi compound (100 ug) was administered to rabbit eyes via a single intravitreal injection. At 24 hours post injection, all eyes were collected and frozen in an optimal cutting temperature (OCT) gel. The frozen block was cut into sections and stained with Hoechst. sd-rxRNA was present throughout the retinal cell layer after intravitreal administration. Fluorescence was detected using a laser scanning confocal microscope.

  FIG. 12 reveals significant silencing of the target mRNA after a single intravitreal injection. sd-rxRNA was administered to the eyes of mice by intravitreal injection (1 ul) at the indicated doses. After 48 hours, retinas were collected, mRNA levels were quantified by QPCR, normalized to b-actin, n = 5-8 (including data from different studies, graphed as +/− SD relative to NTC) * P = 0.05, ** p = 0.01).

  FIG. 13 reveals significant silencing of the target mRNA after a single intravitreal injection. 3 ug of PPIB or NTC sd-rxRNA was administered to the mouse eye by a single intravitreal injection (1 ul). Retinas were collected 1, 2, 4, 7, 14, 21 and 28 days after injection. mRNA levels were quantified by qPCR and normalized to b-actin. Data from 6 different studies were collected (n = 5-8) to allow sufficient “n” for each data point (graphed as +/− SD relative to PBS in each study) * P = 0.01).

  FIG. 14 reveals significant silencing of the target mRNA after a single intravitreal injection. 3 ug of Map4K4 or NTC sd-rxRNA was administered to the mouse eye by a single intravitreal injection (1 ul). Retinas were collected 1, 2, 4, 7, 14, 21 and 28 days after injection. mRNA levels were quantified by qPCR and normalized to b-actin. Data from 6 different studies were collected (n = 5-8) to allow sufficient “n” for each data point (graphed as +/− SD relative to PBS in each study) * P = 0.05, ** p = 0.01).

  FIG. 15 reveals that sd-rxRNA did not cause vascular leakage after 3 weeks of administration. The sd-rxRNA was administered by a single intravitreal administration (1 ul) of 5 μg of both Map4k4-TEG and Map4k4-HP sd-rxRNA and PBS. One, two and three weeks after administration, fluorescently labeled dextrin was administered subcutaneously prior to fluorescent fundus imaging. Fluorescence fundus angiography revealed no retinal blood vessel leakage.

  FIG. 16 reveals that sd-rxRNA did not cause structural damage to the retina 3 weeks after administration. The sd-rxRNA was administered by a single intravitreal administration (1 ul) of 5 μg of both Map4k4-TEG and Map4k4-HP sd-rxRNA and PBS. Optical coherence tomography was performed 2 and 3 weeks after administration. A representative image shows the structure and thickness of a normal retina.

  FIG. 17 reveals that sd-rxRNA did not impair retinal function 3 weeks after administration. The sd-rxRNA was administered by a single intravitreal administration (1 ul) of 5 μg of both Map4k4-TEG and Map4k4-HP sd-rxRNA and PBS. Dark-adapted electroretinogram (ERG) recordings were taken 3 weeks after administration, revealing similar retinal function after administration of sd-rxRNA and PBS. A record of light adaptation was also collected with similar results.

  FIG. 18 demonstrates an approach for multiple targeted silencing with sd-rxRNA. The silencing activity of several sd-rxRNAs was determined in cells treated with up to four sd-rxRNAs targeting multiple genes of interest. When administered in combination, sd-rxRNAs retained their potent potency, indicating their potential for multiple targeted silencing.

Table 2 represents the 25-mer sequence in VEGF. rxRNAori and sd-rxRNA can be directed against the sequences in Table 2. In some embodiments, the rxRNAori comprises a sequence represented in Table 2.
Table 3 represents non-limiting examples of sd-rxRNA molecules directed against SPP1.
Table 4 represents a non-limiting example of the sequence of sd-rxRNA directed against PTGS2 (COX-2).
Table 5 presents non-limiting examples of sd-rxRNA sequences directed against CTGF.
Table 6 represents a non-limiting example of the sequence of sd-rxRNA directed against TGFβ2.
Table 7 represents a non-limiting example of the sequence of sd-rxRNA directed against TGFβ1.

Example 2: Identification of sd-rxRNA targeting VEGF
The optimal sequence for sd-rxRNA development was identified using a sequence selection algorithm (Table 2). The algorithm selects sequences based on the following criteria: GC content higher than 32% but lower than 47%, homology to a particular animal model (eg mouse or rat), 5 or more U / U Avoidance of extension and / or extension of 2 or more G / Cs, off-target hit scores of less than 500, and avoidance of sequences contained in the 5′UTR.

  The sequence was first developed as a 25 nucleotide blunt end duplex with O-methyl modifications. Such sequences were screened in various cell lines to identify those that were most efficient in reducing gene expression. Several concentrations of RNA molecules such as 0.025, 0.1 and 0.25 nM were tested to determine the preferred concentration. Dose response curves were generated to determine the strongest sequence. These sequences were developed into sd-rxRNA molecules based on the parameters described throughout this application.

Table 8 represents a non-limiting example of the sequence of sd-rxRNA directed against VEGF.
Table 9 represents non-limiting examples of rxRNAori sequences directed against VEGF.
Table 10 represents the results of optimization of the sequence of sd-rxRNA directed against VEGF using various chemical modification patterns.

Example 3: Chemical Figure 19 of the linker, it indicates that the variation of the chemical linker does not affect the silencing activity of the sd-rxRNA in in vitro. Hydroxyproline linker and Riborinka two different a chemical linker, for a plurality of sd-rxRNA (targeting Map4k4 or PPIB), was evaluated in passive uptake assay was used to determine the favorable linkers self delivery . HeLa cells were transfected with sd-rxRNA at 1 uM, 0.1 uM or 0.01 uM for 48 hours in the absence of delivery vehicle (passive transfection). Use of either linker resulted in effective delivery of sd-rxRNA.

The ribolinker used in Example 1 had the following structure:

  Thus, while several aspects of at least one embodiment of the present invention have been described, it should be understood that various alterations, modifications, and improvements will readily occur to those skilled in the art. Such alterations, modifications, and improvements are intended as part of this disclosure, and are intended to be within the spirit and scope of the invention. Accordingly, the foregoing description and drawings are merely examples.

Equivalents Those skilled in the art will recognize, or be aware of, numerous equivalents to the specific embodiments of the invention described herein using only routine experimentation. Such equivalents are intended to be encompassed by the following claims.

  All references disclosed herein, including patent documents, are incorporated by reference in their entirety. This application was filed on September 22, 2009, PCT Publication Number WO2010 / 033247 (Application Number PCT / US2009 / 005247), Title “REDUCED SIZE SELF-DELIVERING RNAI COMPOUNDS”, and February 11, 2009 PCT publication number WO2009 / 102427 (application number PCT / US2009 / 000852), title “MODIFIED RNAI POLYNUCLEOTIDES AND USES THEREOF”, including all drawings and all parts of the description (sequence listing or amino acid / polynucleotide sequence) Are included for reference.

Claims (55)

A method for delivering a nucleic acid to the eye of a subject in need thereof, comprising:
Said method comprising administering to the eye of the subject sd-rxRNA in an effective amount to promote RNA interference by said sd-rxRNA in the eye.   The method of claim 1, wherein the administration of sd-rxRNA is intravitreal.   3. A method according to claim 1 or 2 for treating an eye disorder.   Eye disorders include vascular leakage, angiogenesis, age-related macular degeneration (AMD), choroidal neovascularization (wet AMD), geographic atrophy (progressive atrophy AMD), early to mid-stage atrophy AMD, postoperative cystoid Macular edema (CME), nonproliferative diabetic retinopathy (NPDR), diabetic macular edema (DME), macular edema secondary to retinal vein occlusion (RVO), proliferative diabetic retinopathy (PDR), glaucoma, Neovascular glaucoma (NVG), retinopathy of prematurity (ROP), fibroproliferative retinal disease, proliferative vitreoretinopathy (PVR), epiretinal / vitreous macular adhesion, retinal degenerative disease, retinitis pigmentosa, retina 4. The vascular occlusive disorder, selected from the group consisting of retinal vein occlusion, retinal artery occlusion, retinoblastoma, trabeculectomy failure due to scar formation, and uveitis. the method of.   5. The method of claim 4, wherein the ocular disorder is age related macular degeneration (AMD).   5. The method of claim 4, wherein the eye disorder is diabetic macular edema (DME).   5. The method of claim 4, wherein the ocular disorder is proliferative vitreoretinopathy (PVR).   5. The method of claim 4, wherein the ocular disorder is trabeculectomy failure due to scar formation.   sd-rxRNA is VEGF, MAP4K4, PDGF-B, SDF-1, IGTA5, ANG2, CTGF, HIF-1α, mTOR, SDF-1, PDGF-B, SPP1, PTGS2 (COX-2), TGFβ1, TGFβ2, 9. The gene according to any one of claims 1 to 8, which is directed against a gene encoding a protein selected from the group consisting of complement factors 3 and 5, PDGFRa, PPIB, and myc, or combinations thereof. the method of.   10. The method of claim 9, wherein the sd-rxRNA is directed against a gene encoding VEGF.   10. The method of claim 9, wherein the sd-rxRNA is directed against a gene encoding CTGF.   12. The method of any one of claims 1-11, wherein two or more different sd-rxRNAs directed against genes encoding two or more different proteins are both administered to the subject's eye. The method described.   13. The method of claim 12, wherein the sd-rxRNA comprises sd-rxRNA directed against VEGF and CTGF.   13. The method of claim 12, wherein the sd-rxRNA comprises sd-rxRNA directed against VEGF and PTGS2 (COX-2).   11. The method of claim 10, wherein the sd-rxRNA is directed against a sequence selected from the sequences in Table 2.   11. The method of claim 10, wherein the sd-rxRNA is directed against at least 12 contiguous nucleotides of a sequence selected from the sequences in Table 2.   17. The method of any one of claims 1-16, wherein the sd-rxRNA comprises at least 12 contiguous nucleotides of a sequence selected from the sequences in Tables 3-8 or 10.   11. The method of claim 10, wherein the sense strand of sd-rxRNA comprises at least 12 contiguous nucleotides of the sequence of SEQ ID NO: 1317 or SEQ ID NO: 1357.   11. The method of claim 10, wherein the antisense strand of sd-rxRNA comprises at least 12 contiguous nucleotides of the sequence of SEQ ID NO: 1318 or SEQ ID NO: 1358.   The method of claim 10, wherein the sense strand of sd-rxRNA comprises SEQ ID NO: 1317 and the antisense strand of sd-rxRNA comprises SEQ ID NO: 1318.   The method of claim 10, wherein the sense strand of sd-rxRNA comprises SEQ ID NO: 1357 and the antisense strand of sd-rxRNA comprises SEQ ID NO: 1358.   The method of claim 10, wherein the sense strand of sd-rxRNA comprises SEQ ID NO: 1379 and the antisense strand of sd-rxRNA comprises SEQ ID NO: 1380.   The method of claim 10, wherein the sense strand of sd-rxRNA comprises SEQ ID NO: 1397 and the antisense strand of sd-rxRNA comprises SEQ ID NO: 1398.   12. The method of claim 11, wherein the antisense strand of sd-rxRNA comprises at least 12 contiguous nucleotides of the sequence of SEQ ID NO: 948 or SEQ ID NO: 964.   12. The method of claim 11, wherein the sense strand of sd-rxRNA comprises at least 12 contiguous nucleotides of the sequence of SEQ ID NO: 947 or SEQ ID NO: 963.   The method according to any one of claims 1 to 25, wherein the sd-rxRNA is modified to be hydrophobic.   27. The method of claim 26, wherein the sd-rxRNA is bound to one or more hydrophobic conjugates.   28. The method of any one of claims 1-27, wherein the sd-rxRNA comprises at least one 5-methyl C or U modification. A method for delivering a nucleic acid to an eye of a subject in need thereof, comprising:
Administering the rxRNAori to the eye of the subject in an effective amount to promote RNA interference by the rxRNAori in the eye.   30. The method of claim 29, wherein rxRNAori is directed against VEGF.   32. The method of claim 30, wherein rxRNAori is directed against a sequence comprising at least 12 contiguous nucleotides of a sequence selected from the sequences in Table 2.   32. The method of claim 31, wherein the sense strand of rxRNAori comprises at least 12 contiguous nucleotides of the sequence of SEQ ID NO: 13 or SEQ ID NO: 28.   32. The method of claim 31, wherein the antisense strand of rxRNAori comprises at least 12 contiguous nucleotides of the sequence of SEQ ID NO: 1377 or SEQ ID NO: 137828.   An sd-rxRNA directed against a sequence selected from the sequences in Table 2.   An sd-rxRNA directed against a sequence comprising at least 12 contiguous nucleotides of a sequence selected from the sequences in Table 2.   An sd-rxRNA comprising at least 12 consecutive nucleotides of a sequence selected from the sequences in Tables 3-8 or 10.   37. The sd-rxRNA according to any one of claims 34 to 36, wherein the sense strand of the sd-rxRNA comprises at least 12 contiguous nucleotides of the sequence of SEQ ID NO: 1317, 1357, 1379 or 1397.   38. The sd-rxRNA according to any one of claims 34 to 37, wherein the antisense strand of the sd-rxRNA comprises at least 12 contiguous nucleotides of the sequence of SEQ ID NO: 1318, 1358, 1380 or 1398.   The sd-rxRNA according to any one of claims 34 to 38, wherein the sense strand of sd-rxRNA comprises SEQ ID NO: 1317 and the antisense strand of sd-rxRNA comprises SEQ ID NO: 1318.   The sd-rxRNA according to any one of claims 34 to 38, wherein the sense strand of sd-rxRNA comprises SEQ ID NO: 1357 and the antisense strand of sd-rxRNA comprises SEQ ID NO: 1358.   39. The sd-rxRNA according to any one of claims 34 to 38, wherein the sense strand of sd-rxRNA comprises SEQ ID NO: 1379 and the antisense strand of sd-rxRNA comprises SEQ ID NO: 1380.   39. The sd-rxRNA according to any one of claims 34 to 38, wherein the sense strand of sd-rxRNA comprises SEQ ID NO: 1397 and the antisense strand of sd-rxRNA comprises SEQ ID NO: 1398.   The sd-rxRNA according to any one of claims 34 to 38, wherein the sd-rxRNA is hydrophobically modified.   44. The sd-rxRNA of claim 43, wherein the sd-rxRNA is bound to one or more hydrophobic conjugates.   45. The sd-rxRNA according to any one of claims 34 to 44, wherein the sd-rxRNA comprises at least one 5-methyl C or U modification.   A composition comprising the sd-rxRNA according to any one of claims 34 to 45.   48. The composition of claim 46, further comprising sd-rxRNA directed against a gene encoding a protein other than VEGF.   48. The composition of claim 47, comprising sd-rxRNA directed against a gene encoding CTGF and / or PTGS2 (COX-2).   RxRNAori, directed against a sequence selected from the sequences in Table 2.   RxRNAori, directed against a sequence comprising at least 12 contiguous nucleotides of a sequence selected from the sequences in Table 2.   51. The rxRNAori of claim 49 or 50, wherein the sense strand of rxRNAori comprises at least 12 contiguous nucleotides of the sequence of SEQ ID NO: 13 or SEQ ID NO: 28.   52. The rxRNAori of any one of claims 49 to 51, wherein the antisense strand of rxRNAori comprises at least 12 contiguous nucleotides of the sequence of SEQ ID NO: 1377 or SEQ ID NO: 1378.   53. A composition comprising rxRNAori according to any one of claims 49-52.   54. The composition of claim 53, further comprising rxRNAori directed against a gene encoding a protein other than VEGF.   54. The composition of claim 53, comprising rxRNAori directed against a gene encoding CTGF and / or PTGS2 (COX-2).